Hybrid is a multi platform (Linux/Mac OS X/Windows) Qt based frontend for a bunch of other tools which can convert nearly every input to x264/Xvid/VP8 + ac3/ogg/mp3/aac/flac inside an mp4/m2ts/mkv/webm/mov/avi container, a Blu-ray or an AVCHD structure.

Here's a general feature list:

extensive ability to configure x264s setting (with dependency checks)
tagging support for mkv/mp4/mov
chapter support for mkv/mp4/Blu-ray
subtitle suppot for mkv/mp4/Blu-ray
separated audio-, video-, filter profiles, audio&video combi profiles
an integrated bitrate calculator
accepts vc-1 and avc raw input
manual&automatic creation&pass-through of chapters
ability to encode single title/chapters
a job-control
aac/mp3/ac3/ogg/flac/dts/pcm audio encoding with dcaenc/neroAacEnc/mencoder/ffmpeg
filtering through mencoder (+ some resize automation)
acceptable Input: avs and everything that mplayer/ffmpeg can decode
supported video output formats: MPEG-4 ASP (Xvid), MPEG-4 AVC (x264, cuda), VP8 (vpxenc), ProRes
supported audio output formats: dts, ac3, ogg vorbis, mp3, aac, flac, pcm, opus, pass-through
supported containers: mov/mp4/mkv/m2ts/webm/avi, Blu-ray or a AVCHD structure
audio/video pass-through -> can be used for muxing, tagging, chapter editing
a lot of option to automate stuff