The best tool on linux at the moment is avidemux.
It has all the advantages of virtualdub and can do any video and audio codecs you want, and has great visual filter tools for crop,resize, etc...
Megui, staxrip, autogk, etc... are all nice, but avidemux does much more (you can cut, append videos, crop, filters, etc...) and is multi platform.
IMHO it's the best free tool for video conversion, cutting, etc... on windows and linux.
It should be included in your distro's repository. You can also find it here:
http://avidemux.org/
(In this thread you find the latest development build with the latest x264 (build 648 at the moment) for windows.
http://forum.doom9.org/showthread.php?t=108784&page=21)
(Linux devel builds are certainly available around here or you should be able to find some repositories with the latest devel builds, depending on your distro. You can also compile it yourself with the latest x264 if you need it.)