rhofmann:Let me clarify a bit - this server is for home use, and is only being used as a seldom-accessed FTP server and a daily use file server. It is running Server 2003 R2 with 1GB of RAM. I have set up the Windows Graphical client for folding. It is only running 8MB onboard Video (it is a server, after all). Is that the best folding client to run under such a setup?
Negative

. The graphical client will only use one core.. So you're only using 1/4th of your total CPU capacity.
rhofmann: I am not too worried about folding interfering with my file server setup so long as it is set up correctly, but I am unsure of what the correct setup is in the folding. This is the first time I have run a shared processing program, so I want to apply as much of my processor as I can to the folding, but I am unsure how to do that without it interfering with my other minimal tasks the server runs.
It won't interfere.. If you're sitting at the server or logged into the server a lot, then go ahead and run the SMP client.. But it will sometimes just stop and you'll have to manually shut it down and restart it.. And perhaps even send a copy of the log over to the folding@home forums so they can help diagnose the problem.. So the SMP client is very high maint. but if you're willing to put up with it, then go for it..
rhofmann:In addition, would a server with dual P3 processors with 3GB of RAM be effective for folding if that was the only application running on it? Not to sound like a needy n00b full of questions, but I am.

again, the other server would be running only 8MB of vram.
All questions are welcome, it's most likely that other people have the exact same questions. Since the P3 supports SSE, you should run two seperate installations of the regular console client, setting a different machine ID for both, and installing both as a "Service" so they run in the background and stay out of your way. Also since you have a ton of RAM on the dual P3, enable BigWUs (Big Workunits) in the configuration as well.
rhofmann:
Any advice on setup for optimization of folding setup would be much appreciated.
Well, the P3 setup there isn't much you can optimize.. Usually I recommend people just "set it and forget it" running the console client as a service (in the background) where it's never in your way and uses the least amount of RAM possible.. The GUI client (with the fancy molecules) actually uses up a bit more RAM than the console client which is why I usually don't recommend people run it.. People do like to watch the molecule, so if that's your cup-of-tea then go for it.. It will get boring pretty fast, and when it does, switch to the console client to run folding@home with less memory usage.
If you want to see what the molecules look like, grab JMol which is a seperate 3rd party application for visualizing the workunit you're doing.. it will allow you to click&drag the molecule around so you get a good look at it.. The GUI client molecule display isn't very good in my opinion..
Edit: Added Jmol link.. Note that JMol does not work for some SMP workunits since they're very different..
Edit #2: Clarification "you're only using 1/4th of your total CPU capacity." -> Which means that your folding@home client will use anywhere between 0%-25% of your total CPU power.. If you're using 100% of your CPU power doing other things, then folding@home will step out of the way and use 0% (since it is idle priority).. But when the server is idle, on your system, the folding@home won't be able to use more than 25% of your CPU power because the graphical client only runs one core and you have a quad-core system
So the choices for your dual-dual core (quad core) server is:
1) Run the SMP client which will use all 4 cores to run 1 workunit (best points per day, but you HAVE to keep an eye on it, it can't be installed in the background as a service and will always run with a console window so you can watch it to make sure it didn't trip over a bug or something)
2) Run 4 installations of the console client as a service (each in their own directory, different machine IDs, etc.)
3) Run 3 Installations of the console client as a service (each in their own directory, different machine IDs, etc) AND one copy of the graphical client (which you already have installed now). btw, for the console clients, make sure you use Machine IDs 2,3, and 4.. Since the graphical client always uses Machine ID 1 and is for systems with a single 1-core CPU.
Edit #3: The GPU client and the graphical client are TOTALLY different.. Don't be confused by them.. To run folding@home on a graphics card (GPU client), you'll need an ATI Radeon X1600 with 256 Megabytes of RAM or better..
The graphical client is the same thing as the console client (both are CPU clients) EXCEPT the graphical client has a fancy graphical user interface and a visualization of the molecule.. The graphical client doesn't use your graphics card at all for anything other than showing you pretty pictures of the molecule. So there is not much difference between the graphical client and the console client, they both run on only one CPU core.. This is why you need multiple installations for multi-core systems unless you use the SMP client (Multi-core CPU client).