Accelerated Video Compression

Solution 1:

Unfortunately x264 – which is probably one of the fastest h.264 encoders out there – has no GPU acceleration yet. There's a "nice" forum discussion about it.

However, researchers at Uni Heidelberg have implemented x264 with OpenCL support, but I haven't tried this yet. You might want to give it a shot, it also has some examples. Can't try it here because I'm on a Mac.

Apart from that, you will probably need a newer Intel processor and an NVIDIA graphics card because of the proprietary CUDA implementation. I found two pieces of software for this:

MediaCoder

is actually free.

Hardware encoding acceleration (nVidia CUDA & Intel Media SDK)

Badaboom

comes at $40, but doesn't really seem to provide acceptable quality (I've read this in some forums)

And with it comes new features, high-end performance, premium video quality, and graphics acceleration via the latest NVIDIA and Intel hardware!

That all being said, I wonder if these tools actually work with Motion JPEG as input. Doesn't seem so straight from the feature list, but you might just want to give it a shot.