Theora
Theora's own quality CRF goes from 1 to 10, with higher being better quality.
I haven't used Theora a lot so I can't really say much about it. Historically, it competes with x264 and Xvid.
ffmpeg
Use qscale to set CRF.
ffmpeg -i dvd_track.mpg -codec:v libtheora -qscale:v 7 video.ogv
HandBrake
HandBrake accepts quality CRF from 1 to 63, with default of 45.
