If you are looking for something similar to flvtool2 or flvmdi, or you are a command line junky then I strongly encourage you to check out MP4Box. MP4Box has a ton of capabilities, but I’m just going to highlight 4 fundamentals:
- Read file info (basic metadata).
- Split or cut files.
- Merge two or more files.
- Convert to iPod.
Read basic file info from an MPEG-4 file:

Split / extract / cut an MPEG-4 file:

Read the info from one of our splices and make sure we’re getting what we expect:

Concatenate / merge multiple MPEG-4 files:

Merged file information:

Convert to iPod file:

MP4Box is a GPAC project, but they only distribute the source (no binary downloads). If you are like me and not keen to try and get Make to compile the source you can grab a binary from here. One last thing–read the docs–you’ll be amazed.
2 Comments
The link you provide is only to windows binaries. Where can I get an osx binary of mp4box that supports the ipod atom ?
Well here’s one link that Google returned:
http://www.tkn.tu-berlin.de/research/evalvid/EvalVid/mp4box-mac.tar.bz2
You can also compile from source. :-)