The one consideration you will need to bear in mind, is that you're unlikely (or at the least very hard-pressed) to find a decent, high-quality GFX card to fit the small form factor. You may be able to find one specifically, but you will be trading size for processing power and it's likely that the choice is quite limited. Any SFF mobos will also lack many slots (although with reasonable quality on-board sound and the prevalence of on-board gigabit NICs, this may be a non-issue). A quick google search turned up some possible, low-profile GFX cards.

I don't know if your case choices inlclude a PSU, but choice on SFF PSUs is also limited when compared with standard ATX. Mobo may also lack RAID controller if that is something you're otherwise used to. Saying that...a quick visit to overclockers turned up some reasonable mobo choices you could consider.

Best advice I would think is pick out the GFX card you want, make sure you find an appropriate case and PSU (powerful enough PSU is very important!), then pick the mobo, CPU and RAM. You might consider and after-market HSF for your CPU if you plan to overclock (though with a SFF case it's probably best not to). Also it's probably best to go with just one single HDD and optical drive (for power, space and heat reasons) so buy a big enough HDD to start with. There's no differences in any of the technologies except for size (and choice?) so just pick your parts carefully. One of those mobos, your choice of case/PSU, suitable SFF GFX card, one HDD, one optical drive, Vista 64-bit and DX10, 2-4GB of decent, dual-channel DDR2 and your choice of multi-core processor, you should be running Eve premium and the rest reasonably well.

All that aside....go ATX, you know you want to!