There may be gpu transcoders, but I havent really looked into it. I know there are multithreaded transcoders, but usually that feature is not compiled into the binaries that are available. So, to get multithreading [and gpu support] you will probably need to compile the codes yourself.
try adding the ffmpeg option "-vcodec libx264" to the transcoding settings. So if it was:
ffmpeg -ss %o -i %s -async 1 -b %bk -s %wx%h -ar 44100 -ac 2 -v 0 -f flv -
change it to:
ffmpeg -vcodec libx264 -ss %o -i %s -async 1 -b %bk -s %wx%h -ar 44100 -ac 2 -v 0 -f flv -
this encoder is multithreaded, but may need to be compiled from source to be supported...
If your using ubuntu this tell you how to compile ffmpeg and libx264 from source:
http://ubuntuforums.org/showthread.php?t=786095
I have not tried this... My computer is fast enough so far.
An easier option would be to move all of your files to a desktop. If you still want to use your laptop to watch, use subsonic to access your files.