Not sure it does exactly what you want, but it's a great program, and it's free.
MPEGStreamClip
Here's some of what their site says.
"MPEG Streamclip can save edited movies as MOV files, and (when possible) as AVI or MP4 files. Edited MPEG-1 or MPEG-2 files are saved as MPEG or TS files.
MPEG Streamclip can also convert MPEG-2 transport streams into muxed MPEG-2 files, for immediate burning at full quality with most DVD authoring applications; it can also demux MPEG-1 and MPEG-2 files and transport streams with MPEG, AC3, PCM audio to M2V and AIFF (or M1A or AC3) files, for immediate burning at full quality with DVD authoring applications. A special demuxing option is available for use in QuickTime Pro: this application does not work well with M2V files, but MPEG Streamclip can write a special "unscaled" M2V file that preserves full video quality.
MPEG Streamclip can handle files and streams larger than 4 GB, split in any number of segments, or with multiple audio tracks, and can also optionally handle timecode breaks. It is compatible with MPEG-1 and MPEG-2 video, MPEG layer 1/2 (MP1/MP2) audio, AC3/A52 audio, and PCM audio.
The player included in MPEG Streamclip lets you preview the files and transport streams before doing the conversion; it also lets you visually set the In and Out points for the conversion so you can convert just the part of the file you are interested in, and also cut commercials and other unwanted parts, or edit the stream and join two streams with Cut/Copy/Paste"
Hope that helps,
