Pricey but works well

I use this along side Handbrake. This can merge 2 or more files together into one .m4v file which is what I needed. I have had issues in a few cases where I had to convert each of the separate files into m4v with this app first then re-encode them together to combine them. It works pretty fast and works with many codecs. WMV files need to have flip4mac installed first prior to opening this app to convert those to m4v. (when I say prior I mean before you encode them, not before you launch this app for the first time).

This also has support for AppleScript which is nice. I put in a script to batch add files within a folder and it worked great.

nobodyhasthisnicknameyet about Turbo.264 HD Video Converter