Interesting question.
As my system is relatively slow and the GUI eats some CPU cycles, this is a nice idea!

If you're under Windows you can simply minimize Foldit to the taskbar and it won't use up CPU cycles for graphics. This doesn't apply to the Linux and Mac version, I think.

I have another reason. I try to control FoldIt through Remote desktop, but limited by 512 Kbit/s internet connection makes it just impossible. I can't see content of FoldIt window. After some blind attempts i stop script execution, restore best, save solution and share it. This was very complicated.

I know, that there is an option to launch fold.it with low priority, something like "foldit.exe -low".
Maybe there are some other options.
A console option, like the BOINC client (for Rosetta) already has built in would be useful, by all means; especially for multi-start-puzzles.

@vakobo:
When running fold.it minimized, I use the task manager to check if a script has ended.
The CPU usage drops about 10-20%.

My problem is in the channel bandwidth, not in CPU performance.

Yes, but if foldit runs minimized, and you just have the task manager visible on a plain desktop, there is not so much data to send.

Sometimes speedups can be gained by sacrificing some image quality as well. Since the graphics on foldit are not essential to using the program quite often.

If you do not have the software for your graphics chipset to make these changes, consider a tool such as ATITool (for ATI graphics cards) or RivaTuner (for Nvidia cards)

RivaTuner can actually let you save per game profiles, so you can set up 2 different ones such as "foldit_playing" and "foldit_away" with "foldit_playing" you can leave default options on for better looks, with "foldit_away" you could turn off options to favor better performance. I'm not that familiar with the latest ATITool

There are a lot of options which can be disabled, and that can lead to rather significant increases on lower end hardware. Also consider dropping screen resolution and color depth (800x600 at 16bit is still very usable for most people, and much easier on your graphics hardware)

Another option is to set up screen macros on the remote machine, which will automatically do things that you commonly wish done. You can then run these from a command line, rather than use all of your bandwidth rendering images.

Yet another option is to use aftermarket VNC software that can be easily adjusted to send lower resolution frames, or send frames less frequently.

How about changing the window title bar?
This can easily to included, so foldit can be run minimized and you can get some brief info about your score by just mousing over the minimized window.
Many download/converting programs do it this way.
They report their status in the wndow title bar.

http://fold.it/portal/node/987847

At the moment, the title bar just reads "foldit".
There is enough space for some score digits, and a hint, if a recipe has finished.
WinAmp for example shows track number, interpret and title.

@Crashguard303: - nice suggestion, it would be great to check on progress in this way.

I use Ultr@VNC and max i can do is getting autosave-best-xxxxx through file transfer feature.
This is because of connection speed limitation ~120 kbps i have with my remote desktop.
I hope that console version will allow more control options such as arbitrary script execution, saving and uploading solutions.
Or may be this can be done by web-interface to foldit client?

According to Pletsch's ideas dealing with imnage quality, I have a feature suggestion, which could be useful, as long as there is no console version and make the game more stable: adjustable fps.
http://fold.it/portal/node/987893