1. How to: Clean install Windows 7 (64 bit) on Alienware Desktop

This is how I rebuild the OS and system software on an AW desktop system.

This is not the same as re-imaging the system back to initial Dell factory software install (like with Alien ReSpawn or Dell DataSafe Local) with the Recovery Partition.
In fact, this procedure will permanetly delete and disable that functionality.

So, if you are a new user, and wish to do a Recovery instead (and/or wish to keep the Recovery functionality for use later), just watch this video and follow the steps on your system:

http://www.youtube.com/watch?v=7LNIPkqsQy8

For many users (with a working Recovery partition) this might be a better option. It will easily reset machine to it's original factory install software and OS config. Just remember that the original Win7 was RTM version, and drivers, etc. will be old versions (from many years ago).

Rockstar Natakuc4 has created this Factory Restore guide for Windows-8.1, which includes creating a Restore USB Flash drive (whether you use it now or not). I recommend everyone create the Recovery Discs, especially if you received no physical media.

With that out of the way, let's get to THIS procedure ...

This procedure is derived from the Official Dell recommended procedure (like for Inspiron and XPS) , but specifically tailored toward Alienware Desktops by me.
It has been successfully used and verified many times by various users. I wrote this long before the Alienware Team started writing their versions.
Read through once completely before starting.

Backup all important data files to a separate USB HDD or flash drive and remove from system for safe-keeping.
Be sure you have all your legit software install CD/DVDs and keys/serial numbers.

Unplug everything except keyboard, mouse, and monitor. Connect all to the ports on the back of machine.
Connect to good UPS (Battery Backup) to deliver good clean un-interrupted power (and enough of it).

Turn off machine. Unplug the MIO-Board communication cable that is connected to the USB-1 header port on the motherboard. On the Aurora, it is along the bottom edge.
Note which wire colors are where so you can put is back on exactly right later.
Do not remove or install side cover with the power on. You can leave it off for now if you wish.

Set BIOS Options
Generally, you can use BIOS Defaults or set hardware options as per your requirements.
Most people want a normal (non-RAID) Hard-Disk-Drive config, so set:

Integrated Devices / Config SATA 1-6 as: AHCI

Save and Exit.

I like to start with a completely blank/raw HDD/SSD (uninitialized and no partitions). At this stage, having only the main bootable OS C: drive connected to controller is usually better.

Begin Windows Install

Insert Dell-AW OEM Windows-7 (64 bit) with original (black) DVD-ROM first. Reboot as required until finished.
In you need a disc, call Dell by phone or order one from here:
https://www.dell.com/support/diagnostics/us/en/04/nondiagnostichome?c=us&l=en&s=bsd&DoNotRedirect=y&redirect=1

After the Windows-7 First-Time-Setup is complete, install the latest Dell drivers (from File Area at support.dell.com ... for your Service Tag)

NOTE 1: I also like to find the required files this way http://ftp.dell.com

This order is important:

Intel Chipset Drivers (must be installed first) .

- For Aurora-R1, I use file INTEL_CHIPSET-SOFTWARE-A03-R239508.exe
Video Drivers
Audio Drivers (Realtek on-board or Other)
Broadcom Gigabit Ethernet (optional if using Microsoft bundled drivers instead)
SIL-Silicon Image (eSATA External HDD Driver) .

- For Aurora-R1, I use file Silicon-Integrated-Systems_S_A02_R235001.exe
JMicron Sata Controller (For optical drives - Area51 Only)

Ignore driver updates from Windows Update. Drivers should some from Dell.
- Or they can come OEM manufacturer (ie. Creative for X-Fi audio card).

Install any missing Microsoft .Net Frameworks versions 3.5, and 4.0 (just Frameworks ... NOT SDKs). Dot Net v3.5 includes support for apps using v2.0 and v3.0.
- This is so Command Center and any other .Net apps will install and work properly.
- Use Microsoft Update. If you need them, they will be offered. Also get the .Net Service Packs.
- Or, see http://www.asoft.be/prod_netver.html

At this point. the Device Manager should be free of errors (all devices should have proper drivers loaded).
Now would be a good time to backup the main drive (C: partition, etc.) with a good Image Backup (like Acronis) to a separate HDD.

Shut-down Windows (Turn off machine). Re-connect the MIO-Board cable to the USB-1 header port on the motherboard.
Re-install side cover. Turn on machine and boot back into Windows.
Windows will detect the MIO-Board, but it's not a conventional Plug-and-Pray device, so you won't get the usual "New Hardware Detected" prompt.
One way it appears is as "Gaming Desktop" in the Unspecified section of "Devices and Printers". Other parts are scattered throughout Device Manager.

Install latest AlienWare Command Center (v2.8.9.0 is the last version that supports Win-7). Don't install a version older than v2.6.17.0 (or it will try to back-flash the firmware on your MIO-Board).

The Intel Storage software (Intel-RST) is optional in a non-RAID environment.
If running a RAID HDD setup some say it's recommended. Install Intel RST 9.6.0.1014 (or latest newer version).
Once installed, it replaces the Microsoft HDD driver and CANNOT be un-installed or removed. Even when you think you are un-installing it ... it's the front-end interface that's removed and the core-driver stays behind.
The Intel ICH-10r SATA hardware RAID solution works from the BIOS. The Intel RST software is just a way to monitor and change RAID parameters from inside Windows (but not required for RAID operation).
If trying to use external eSata drives with port-multiplexing, (due to incompatibilities) you
should probably skip it. Other RAID controllers might also have a problem with it installed.
I'm running a Samsung 830 SSD these days. System works great in AHCI-Mode and with NO Intel-RST installed (now or ever). System just uses the bundled Microsoft Windows SATA drivers.

I've always had this opinion of Intel-RST. However, I just found this on a knowledgeable IT pro's (in HDD/NAS/RAID field) forum post:

Advantages of the Intel-RST Software installation:
1. AHCI and RAID: monitoring of some details regarding the drives, which are connected to the Intel SATA AHCI resp.RAID Controller
2. only RAID: creation, repairing and modification of a RAID array from within the OS
3. only RAID: enabling of the "Write-Back-Caching" feature (boost of the write performance in RAID mode)

Disadvantages of the Intel-RST Software installation:
1. extension of the boot time
2. additional demand of resources (the IRST Service usually runs permanently in the background)
3. possible increase of system instability (some IRST Software versions have severe bugs)

And finally, there was a major driver architecture change at Intel-RST v11.5.0.1149 and later. So, if you must use it (please don't) and the latest version doesn't work, try an older version like v10.1.0.1008.

Install Microsoft Security Essentials (or your favorite Anti-Virus/ Anti-Spyware)
Windows Firewall is handling the software firewall duties
- If not already done, put machine behind a good (ie SPI) hardware router/firewall ASAP.

My machine originally came from Dell with McAfee, CyberLink PowerDVD Player, and Nero. If you still want them, you might be able to get them from "My Dell Downloads" or "My Locker" in area protected with your main Dell Account. However, my preference for these kinds of apps is instead Microsoft Security Essentials, VLC Player, and ImgBurn (all free, BTW). I installed them instead.

Go ahead and install all the missing Important and Recommended Windows Updates (but remember, no drivers).
Use Acronis again (or similar) to make a complete Image Backup of your main drive or partition.

Now, it should be safe to visit websites other than dell.com and microsoft.com .
- To prevent problems stick to legitimate websites.

Notes about Partitions:

My Aurora (R1 - X58) came with the following partitions:

Dell Diagnostics (hidden) - 40mb
Dell Recovery (hidden)
OS (main C: drive where Windows runs from)

First ... There is apparently no way to manually or clean install Windows and keep the functionality of the Dell Recovery procedure.
In my opinion, this is not important because of several reasons:
1. Dell DataSafeLocal has proven to be unreliable in day-to-day operation.
2. It has the potential to become corrupt (partial HDD failure, etc.). Even Dell's tech. support has acknowledged this.
3. It becomes outdated quickly (driver versions, missing Windows patches, etc.)
4. Again, even if you leave Recovery Partition in place and get Windows 7 running (with clean install), there is no established way to use it again.
5. I find Acronis (and it's ability to do "bare metal" partition backups and restores) better suited to my needs.

In the rare cases when you need to run the Linux based Dell Diagnostics, you might as well run the latest version ... that you downloaded and burnt to a bootable CD-R. And yes you should run it ... it's the best way to check all your hardware (including the MIO-Board) from outside Windows.

When you go to fresh or clean install Windows 7, (using Pro or Ultimate) if the drive is completely blank (no existing normal, hidden, or OEM partitions), it will install it's own hidden "System Reserved" partition (as the first partition ... it must be first). This uses WinRE for BitLocker and other emergencies. The System Reserved partition is not required for proper operation (notice you don't get it from the factory, and Windows works fine).

I guess the bottom line is that you can only have one or the other in that first hidden partition. Since lower Home versions don't use Windows "System Reserved" partition ... to make everything the same, Dell decided to put Dell Diags there. Plus, a lot of people lose their CDs, so it's handy to have Diags load from BIOS boot menu. So, which-ever one you put there, it will be OTHER one that you need the bootable CD/DVD for.

MIO-Board Notes:

I have installed and re-installed Windows on my Aurora many times and never had a problem. However, some users have had problems with their MIO-Boards (they get locked up) after clean installing Windows (they weren't using this guide, and might have done other things incorrectly, but still ... it warrants caution I suppose). Therefore, I have added the additional steps to dis-connect the MIO-Board from the motherboard while Windows is installed and setup for the first time. While this step is likely un-neccessary, it's one way to side-step any potential issues. (Added 3-2-2012)

 -  See my post here for additional MIO-Board & Command-Center info and trouble-shooting

General Notes:

When you boot the Windows 7 (64bit) DVD to start re-installation (press F12 if you need to) ...
1. Select the Full install option (not upgrade or repair)
2. Use the Advanced option on the drive selection menu to delete all existing partitions (on your install drive only) first.

Contrary to what all the online Dell docs say, DO NOT update your BIOS at this time. First of all, you should only update your BIOS if there is a reason to do so (don't fix what's not broken). Second, updating your BIOS from inside Windows is just asking for a bricked or permanently killed motherboard. Only update your BIOS if talking to Dell on the phone, so that when it bricks itself, they can send you a free new motherboard (because they made you do it). If you are out-of-warranty and absolutely must update your BIOS to fix a definite problem addressed in a BIOS update, you should do it the more complicated way; create a bootable (DOS or Linux) flash drive and flash the BIOS - OUTSIDE OF WINDOWS.

If the BIOS update utility program will only run under Windows, I suggest Safe Mode. If it won't run in Safe Mode, (and you are prepared to buy a new motherboard if it bricks itself) your only option is inside Windows proper. At least, shut-down as many programs, TaskTray utils, and Processes as possible (especially things like Anti-Virus monitors, etc.). You can also try a Windows Clean Startup but you are really on your own at this point. You have been warned.

Due to availability of hardware drivers (and custom AW apps), Alienware machines are only 100% compatible with 64-bit versions of Windows 7. If you choose to install a different version of Windows-7 (other than the version that came with the machine) it must be 64bit. The best way to get from Home Premium to Pro or Ultimate is to use the built-in Microsoft Windows AnytimeUpgrade procedure.

This basic procedure should work on any AW desktop. However, if newer desktops have UEFI , additional drivers might need to be loaded from USB flash drive before the Windows Install can detect all required hardware and actually get started (especially if using RAID Mode).
I don't have an Aurora R4, but according to user forum feedback, setting the BIOS boot options like this should allow a Win7 DVD or USB to boot: SATA Mode = AHCI Mode , Boot Mode = UEFI, SecureBoot = Disabled. Or, see this article.

The Dell-Alienware Team finally published their own instructions in 5-2012.
They are here: http://support.dell.com/support/topics/global.aspx/support/kcs/document?c=us&cs=19&docid=549172&doclang=en&l=en&s=dhs 
 
And here: http://support.dell.com/support/topics/global.aspx/support/kcs/document?c=us&cs=19&docid=536193

If I missed anything, let me know and I will add it.
Updates: 
05-22-2015 - Added info 
03-01-2016 - Dropped use of Acronis-2010. I use Macrium Reflect for everything now.
05-01-2016 - My Aurora-R1 has been upgraded to Windows-10 Pro (64bit) for free