abieross,
The only operating system Dell is currently installing on any of the Dimension models is Windows XP [Home or Pro]. You can install Windows 2000 or Windows 98 on a Dimension 4400 without technically voiding your warranty if you wish. Dell won't support either of these operating systems on your machine though, so if you were to buy two systems and install either one then all of your software support is effectively transferred to Microsoft. Some people who post here regularly say this is just an easy way for Dell not to support their own computers and customers and on some levels maybe it is, but speaking as someone who has done tech support for one of the major PC manufacturers I can factually state that this policy is the result of legal/software licensing agreements the PC manufacturers have with Microsoft.

As far as conflicts go, keep in mind that the components used to make a Dimension 4400 were built and released a few years after Windows 98 was declared discontinued by Microsoft. This means it's possible that there may not be Win 98-compatible drivers for all your devices. Aside from a few bells and whistles (and the obvious graphic interface), Windows XP is very similar to Windows 2000 so odds are you'll be able to find any device drivers you need on the manufacturer web sites if Win 2k doesn't have native driver support for them. Just some things to consider.