Right now I use
SUPER to encode H264 videos in a .mov wrapper.
At low bitrates though regular QT movies look pretty bad using Sorenson 2 which is also part of Super.
I know some others like Jay were happy awhile back with Sorenson 3 Compression suite for Quicktime. It seems to do a nice job at low bitrates which is where Quicktime often falls short.
Any new software recommendations for low bitrate quality Quicktime video?
John