The previous topic suggested XMediaRecode. I tried it but it screwed up the subtitles because it somehow lost the embedded font causing the re-encoded video to have gigantic, retarded-looking subs.
I also tried handbrake and it seemed to be what I was looking for, though I have to test it more thoroughly. Also got FormatFactory but didn't try it out yet.
Edit. FormatFactory seemed otherwise good but unfortunately it also screwed the subs. It didnt lose the font but the texts became really big and the letters were spaced out so that the subs would sometimes end up filling 4 rows (lol) making the video itself unwatchable. Any tips? I didnt notice any way to change subtitle-specific options in any of these programs. This far only handbrake got them right. The subs are normal styled .ass subs with an embedded font.
Edit2. After more testing, I'd say handbrake is the best one. Gets all the subs right and if you fiddle with the advanced options you'll get really good quality. (although the encoding takes some time... 25 minutes per episode on a 4,00GHz dual core. Well, I got time so that's no biggie) Had no problems re-encoding a 10 bit test file either.