Here are some I use (my favourites)

1. Tsunami MPEG DVD Author Pro (for converting a VIDEO_TS folder to an MPG file (without re-encoding / super fast)

2. Womble MPEG Video Wizard for frame level native MPEG editing and exporting

3. VideoRedo (QuickStreamFix utility) to "FIX" an MPEG file containing non sequential PTS (I recommend using this before demuxing the MPEG) this will usually re-arrange PTS to be sequential, to avoid audio sync issues when demuxing.