What kind of hardware could I get (CPU type, Video Card, MotherBoard, etc...) to aid in the conversion of video files (not the playback of video files)?
I generally use AVS products (avsforyou.com).
I can't give you any specific hardware recommendations.
In your case I think it's mostly CPU that you can improve. Just buy the best you can get for money — Intel's i7 are quite the workhorses now. Then again, it all depends on the codec. If you have a quad core and a poor codec, it will only use 25% of your CPU. I've experienced this myself: On the same system (Intel quad core), converting 4 videos with the MPEG-4/h.264 reference encoder took almost the same time as 1 video.
Also, some video codecs enable GPU acceleration, but only if they are compiled that way. I think
Also, a faster hard drive will help you edit/copy the material faster. I often transcode .mkv files to .avi and here, changing my work disk to an SSD really paid off.
In general terms (not AVS-specific): Monitor your system while your transcode is running.
If your CPU utilization is high, you're waiting on your CPU. A faster one or one with more cores (assuming software support for more cores) will improve your transcode times.
If your CPU utilization is low, you're probably waiting on disk access. The biggest improvement for this will be to ensure that a second physical disk is involved. Reading from one, writing to the other. Beyond that, faster disks.