Video Rotator is a relatively simple Mencoder front end or GUI with most settings hardwired into the app. Unfortunately like many apps from this development team, installation isn't so great -- an older copy of MSCOMCTL.OCX is included & registered with Windows in the program's folder... a shared file, this could break other apps that require a newer version, & removing the app removes the now shared file as well, likely breaking any other apps using it. OTOH if you instead rely on a copy of MSCOMCTL.OCX installed & registered with Windows as it should be, forgetting about or deleting the copy that comes with Video Rotator, it's a harmless enough portable app.
http://www.microsoft.com/en-us/download/details.aspx?id=10019
Mencoder, like the related media player & ffmpeg is pretty much standard fare that should handle pretty much any usual video formats, & I had no problems opening video files or converting them. Results OTOH both varied &, because I couldn't set the encoder or its settings, weren't up to my standards... A simple 720 x 480 mjpeg test avi was rotated, but the result had the wrong aspect ratio [it was converted to 16:9], higher compression, & wouldn't play in Windows Media Player, though it worked fine in VLC. AVC/H.264 video rotated & saved as an AVC video worked as expected, although it was lower quality because of the reduced bit rate -- again no way to change that.
I could be very wrong, but I suspect Video Rotator was originally created for those folks with handhelds that didn't automatically rotate the screen display -- I have an old MP3 player where the video has to be rotated, & while as far as the player knows everything's the same as before [it keeps its original orientation], you just turn it on its side to watch the video play. I used to use VirtualDub, which does an excellent job with the rotation, but available encoders are a bit rare, so I just saved it to a near lossless intermediate format & encoded elsewhere.
You can get Mencoder itself here, & the next two links talk about using it.
http://www.videohelp.com/tools/MPlayer
http://www.mplayerhq.hu/DOCS/HTML/en/mencoder.html
http://www.mplayerhq.hu/DOCS/HTML/en/encoding-guide.html