There are a lot of great online converters available to encode video.  They may take a while and might not be able to process your file, but you get what you pay for!

http://w12.media-convert.com/convert/
http://www.mediaconverter.org/
http://www.zamzar.com/
http://www.mirovideoconverter.com/
http://handbrake.fr/

If you have Adobe you may already have a video encoder called “Adobe Flash Video Encoder.”  It will only encode videos to the .FLV format and won’t work for every format, but is a bit more reliable and faster than online encoders.

If you’re on a Mac I really like the free application iSquint. It works on a wide range of formats and has some advanced options as well H.264 encoding.  It will only convert to the .Mp4 format, though.

For PC I’ve heard good things about dvdvideosoft which has a very impressive listing of tools.

For both platforms there is also a powerful free application available called squared 5, and MPEG Streamclip.

Another trick for encoding video files as well as transferring them is to go through youtube first.  Some of the HD encoding from youtube isn’t that bad.  Once it finished you can download it using:

http://www.downloadhelper.net/