I did a little more research on the state of CUDA. One common feature of my web searches was that CUDA enabled encoders did provide a speed boost. The second thing that came to mind though was the beta nature of most of these apps. They all pretty much did not provide the flexibility that any serious encoder needs at this time or the hobbyist probably doesn't need the speed boost.
As for Adobe CS4, it's GPU acceleration is OpenGL based so even ATI cards work with it. It does enhance some aspects when working with files. Most noticeably, zooming and rotation of images in Photoshop CS4 vs previous versions (again this works for all cards that support OpenGL 2.0). On my laptop, Photoshop CS4 was noticeably smoother in it's zooming with a C2D 2.8ghz and 8600m GT. The speed improvement on my Q9550 desktop was negligible in Photoshop but I have 8GB of RAM as well as an overclocked 3.6ghz CPU. Slower CPU's may benefit but again it won't matter if your GPU is ATI or nVidia so long as it supports OpenGL 2.0.
It's also said to speed up After Effects, though I don't know to what degree since I have not used that program.
Where it should really shine is in Adobe Premiere CS4 with the RapiHD plugin. RapiHD is made by the same company that produced Badaboom. Considering the beta nature of Badaboom, I do not currently have high hopes for RapiHD. I did find one test for RapiHD but to be honest, I felt the test did not provide enough information to make a truly informed decision.
RapiHD test here. TMPEG 4.0 test. For one thing, parameters and settings is severely lacking (in the RapiHD test). For another, anyone who is even contemplating buying Premiere and then shelling out even more money to buy a plugin for it to accelerate video is not going to be using a dual core CPU, though it's more likely with TMPEG. They'll be using a quad core CPU and 4GB of RAM. TMPEG is also not exactly a pro level app and more for home hobbyist who do not care as much about quality or power. Either way I'd love to see what CUDA does on a machine built with video encoding in mind rather than the ones I've seen in these previews.
Either way, Adobe CS4 is very very very expensive and not for the common person. Heck, my copy is somewhat of a grey area since I use my work place's license at home...I certainly would not spend that kind of money on a pro level app for home use. But having access to a copy of Adobe CS4...the GPU acceleration is not worth buying an nVidia card for at this time.
Obviously I've stumbled accross nVidia demonstrations showing how great CUDA is in helping video acceleration but doing searches by other people show a severe lack of information and testing available. The software is likely in beta form or works only in very specific situations.
At this point in time it is stupid to spend extra money to buy a better video card in the hope it will help video encoding. The software is simply not ready to support the hardware yet. Get the best CPU you can now and when the software is ready, then buy whichever is the best video card that will help video encoding. And likely it will be an nVidia card. At that point, video cards should be cheaper and faster so you get more bang for the buck instead of being an early adopter who buys a product not quite ready for prime time.
To be honest, when converting most of my video, it is usually done when I don't need the computer. A lot of times I will queue a few files to encode and start the batch before I go to sleep. Honestly if you budget your time correctly, encoding times won't matter as much. That is assuming your computer is not so slow that it takes hours to encode one file.
HendrixFan and LokutusofBorg has it right, the biggest thing is to make sure you have a fast hard drive, a fast quad core CPU and a minimum of 4GB's of RAM. Last on the list should be the video card.