Start on deciding what CPU you want in it (AMD or Intel, and which architecture).
When you know that, set minimum specs for the motherboard (number of RAM slots, number of PCI slots, onboard sound?, onboard networking?, onboard video? etc.). (*)
Based on those specs, select the best possible motherboard.
Once you have that determined, select RAM, harddisk, and CPU.
Then select the extra
cards needed (video, network, sound) based on your requirements and budget.
(*) I prefer to never use an onboard videocard. Video changes rapidly, so you're likely looking at getting a new videocard several times during the lifetime of the machine.
In your case, you have to be extremely careful. Linux hardware support is extremely lacking especially for modern video and soundcards!
Of course you also need to select a case to hold it all.
Go for the biggest powersupply you can get, and select a case that's as large as you can comfortably store (it's likely to get crowded over time as you add more and more stuff).
[ July 30, 2004: Message edited by: Jeroen Wenting ]