My favorite fire-and-forget encoding is Grass Valley ProCoder, which will run in parallels (although it'll run faster booted into bootcamp).
The latest version of Compressor fixes some long-time bugs around quality in 2-pass mode with fades. But when you really want to push bitrate down without getting blocky, ProCoder's my go-to tool.
If you really want to get hands on, CinemaCraft lets you do a lot of segment-based reencoding, but you need to be willing to put the time into it to get good results.
My compression blog:
http://on10.net/blogs/benwagg/
My compression class at Stanford:
http://digitalmediaacademy.org/courses/video-compression-training.html
