I'm having a really hard time figuring out which video cards are most qualified for this type of computing. Does Fermi beat out ATI's 5000 series? On paper, it appears ATI can perform more GFLOPS, but what about in practice? Any advice or information or links to advice or information would be much appreciated.

I'm having a really hard time figuring out which video cards are most qualified for this type of computing. Does Fermi beat out ATI's 5000 series? On paper, it appears ATI can perform more GFLOPS, but what about in practice? Any advice or information or links to advice or information would be much appreciated.

The choice of GPU depends mostly on which project or projects you want to run on it.

Questions like:
Does the project have ATI or Nvidia applications (CAL or CUDA)?
Does the project require Double Precision GPUs?
Are you using Windows or another operating system?
In case it's CUDA, does the project already have a Fermi application?
-- This is a requirement on Fermi class GPUs as they do not run CUDA code correctly. Older CUDA GPUs can run Fermi code, though. Yet if the project still has only CUDA applications and no Fermi app, then you can't use your new Fermi card on this project.

And of course, when does Crysis 2 look better, on the ATI or Nvidia card? ;-)

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My advice would be a 58xx or 460, so you are all covered in respect to DP and OpenCL 1.1 :)
@ageless still no gpu message board? :(

I know I've already posted about this , but how hard can it be to make a GPU message board just for gpu projects?
THe way I see it, DNETC, MilkyWay, Collatz & GPUGRID make up 62% of the total RAC/credits. If you throw in SETI, AQUA, PrimeGrid & Einstein, which also have GPU apps, let's say half, you have an aditional 13% for a total of 75% (looked at bam graphs).
So, apparently all work that is done at BOINC, 75% is made on the GPU.
The same thing I see at folding, but around 10% is done on the CPU.
Why is it so hard to make a separate message board, or are you waiting for 99% of the research to be done on the GPU?

Define "best".

The fastest GPU for BOINC projects is probably one you can't afford and uses way too much electricity :)

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Thanks everyone. Let me be more specific:
I'm aiming for around $200 to spend here, sometime before fall but maybe I'll wait depending on finances, in which case I might wait for ATI's Southern Islands series to see what improvements they make.
I want to do something to help better understand climate change if possible, though I know climateprediction.net doesn't offer GPGPU (or does it?)
I was thinking I'd find the best GPU for double precision performance, since that seems to be where GPUs render the smallest performance.
But then I saw a link stating that 58xx series ATI GPUs don't do OpenCL as well as even GT200-based nvidia GPUs, which made me think they might not be as good for gpgpu in general.

What I really, really, really want is a shootout of modern GPUs entirely focused on OpenCL and GPGPU in general. Pluses, minuses, all laid out in layman's terms if possible.
Oh, and my system:
Ubuntu 10.04
AMD Athlon II x4 635 @ 3.04 Ghz
2x2 GB DDR3-1333
Biostar A785G3 Motherbouard

You're right. Climate prediction doesn't use the gpu for it's models.
With the current Millennium models, it's far more important to have up to date drivers from the card maker, especially OpenGL, as this is what is used for displaying the graphics.

I'm using cheap GigaByte GeForce 8400 GS cards in my 2 Q6600 machines.

If you want the amount of detail that you mention in your last paragraph, then you may need to search the net yourself. The people posting here are just volunteers, and would have to spend time searching.

Fair enough. Sorry if that sounded like a demand. It was more of a wish, because I have looked high and low on the interwebs and come up dry when it comes to a decent comparison of ATI and nVidia GPUs' GPGPU performance. I was just wondering if anyone had had more luck than I.

No. I didn't consider it a demand, more of a 'big ask'.
The problem with asking here, is that this site is for people with problems, and only those with gpu problems would look at this thread.
Also, those answering questions are only a hand full of people who feel inclined to help others, and aren't necessarily those with lots of knowledge on all things BOINC.

You may have better luck asking on the boards of those projects that have gpu apps, who may have a larger collection of knowledge on what's best, at least for that project. Then combine the data for all projects which have provided info.
Also, projects change, so a thread at one of those boards may keep you up to date with changes/improvements.

Still, keep an eye on this thread too. You never know ...

Fair enough. Sorry if that sounded like a demand. It was more of a wish, because I have looked high and low on the interwebs and come up dry when it comes to a decent comparison of ATI and nVidia GPUs' GPGPU performance. I was just wondering if anyone had had more luck than I.

Recently I started looking just for FLOPS/TDP Max ratio :)
http://en.wikipedia.org/wiki/Comparison_of_AMD_graphics_processing_units#Evergreen_.28HD_5xxx.29_series
http://en.wikipedia.org/wiki/Comparison_of_Nvidia_graphics_processing_units#GeForce_400_Series
http://www.gpureview.com/show_cards.php?card1=626&card2=633
http://www.notebookcheck.net/Comparison-of-Graphic-Cards.130.0.html