IMHO, going small is definately the way to go! There are several great motherboard options from Asus, Gigabyte and DFI that, to me, qualify as "enthusiast-level" products. Start off by looking for a board with a PCI-E 2.0 slot. This way, you can run all of the current GPU technology. Then look for a board that has the type of connectivity you need already ON-BOARD. By doing this, you'll eliminate the need for add-on/expansion cards...especially if you're going to run a beefy GPU that takes up the space of two slots. Even if you're looking at doing only a "minor ammount of gaming", the on-board GPUs of even the best mATX boards out there won't do a game like Bioshock any justice.
As far as chip sets, I would look to an Intel-chipped solution. Intel's newest chipset, the 45-series, supports all of their newest 45-nm CPUs, both Dual and Quad cores. I used to run an EVGA 630i/7150 nVidia based mATX board, but right now, the nVidia mATX solutions do not support all of the 45-nm CPUs, especially the Quad-Core Wolfdales. Also, the Intel 45-series boards run memory in a dual-channel configuration, while the nVidia-chipped boards do not.
Take a look at my LAN Box's specs below. I absolutely love the Asus P5Q-EM m/b! (You can read my review of it
here.) This thing does it all. It does everything I need a PC to do and can game very, very well. It runs cool, runs efficiently and looks awesome. The best bit? It's small enough that taking it with me to a LAN party or a friend's house is really a non-issue. Heck, I got three family members asking if I'd build them something like it!
I really think that the only way I'm going back to ATX is for any application where the pieces just won't fit onto a mATX board, like a truely dedicated, cost-be-damned gaming rig that's running 2 or more GPUs (I'm already planning one for X-58/Nehalem!) Or for when a small-form factor case is simply not big enough, like my Home Media Server project that'll be running a bunch of HDs.
Good luck on the build!
Arvin