The biggest impact i expect the mobo will have on folding is how well it oc's the q6600. There are really cheap mobo's out there that 'support' quads but will not let you get much if any oc due to lack of settings adjustment, etc.
The difference is between maybe a 0-5% oc, and a decent oc'ing mobo of 20-40% oc with the current q6600 steppings.
Hopefully new G0 steppings will either increase the high end of the oc range, or increase the % of cpus' that oc to the high end of the range with perhaps lower volts than the current stepping on the sl9um q6600, or both.
Memory speed is important in that higher bandwidth helps folding performance. High memory speed is more important than tight timings for folding performance. Also, the memory needs to be able to run fast enuf to not limit your cpu oc since none of the quad supporting intel chipsets support a memory divider ie running memory at less than a 1:1 ratio to fsb. Nvidia chipsets allow the memory speed to be decoupled from cpu clocks but i have no experience with them.
You might get away with memory rated at 667 since a lot of it will oc to close to 800 or even better, but I would not recommend anything rated less than 800 if possible. The good news is that ddr2 memory prices have come down quite a bit lately so there is lots of good oc'ing 800 memory out there that will run at 1000+.
you will be able to fold fine atm on 1GB memory, but the price delta to 2gb is not that big atm so i would go for 2gb if the budget can handle the extra $50?. If the rig is only gonna fold and maybe some light duty other work, 1 GB should be ok for now, but new wu types may start to arrive that will need more. If the rig is going to do lots of other stuff incl gaming, video, etc then it would be best to start with 2 gb, and 2gb is prolly 'mandatory' if you are planning on running vista (which i don't recommend).
In fact, if the rig is gonna be dedicated to folding and you don't have a copy of wxp for it already, you can save some money by running linux which is free.
Video is going to depend what you will use it for. Stay away from mobo's with integrated video since they don't usually oc well if at all. On my dedicated folding rigs, i prefer 8 MB pci video cards ... cheap, low power and heat and work in any mobo. I have a few 2MB cards but they limit the screen resolution to 1024x768 in wxp, and less in linux.
If you need good video for gaming, video, then i have no recommendations other than don't plan on GPU folding on the same rig you will be running an smp client.
For dedicated folding only a small ( <40 gb) hdd is required, but sata hdd's are very cheap atm. I can buy a 250 gb sata drive now for less than an 80 gb drive a year ago.
I run my folding (and main rig) caseless but you need to have a safe/convenient place for the caseless rig and its peripherals to sit. Caseless saves a bit of money on case, can take less space and is easier to cool and work on. And it certainly looks ghetto
You can even build it in to something but the mobo needs very good airflow.
I am sure you will have fun planning and then building it