i prefer VidCrop PRO. A very functional and easy software!supports most popular video formats *.AVI, *.WMV, *.MPEG, *.MOV, *.3GP, *.MP4. Result movie file would be avi, wmv, mpeg1, mpeg2, 3gp, mp4 and it will be controlled with width, height, frames per second and other codec properties.
I use it for a long period and haven't got any problems with converting.
you can try it free here http://geovid.com/VidCrop_PRO/