I use Avidemux, it's free, runs in the most common operating systems, and has many useful features.
Edited to add that I also use WinFF to make some conversions (usually when Avidemux cannot open the video), Virtualdub (that has many plug-ins) and Aegisub to make subtitles.
All free.
[edit on 12/9/2009 by ArMaP]

