The first three tools are Windows specific, with the last being cross-platform and especially necessary for linux users.

Super11
Link: http://www.videohelp.com/tools/SUPER
Not well known, but very robust software with good features and overall good functionality.

Riva FLV Encoder
Link: http://rivavx.com/?encoder
Similar to Any Video Converter (listed below). Depending on your needs, compare with Any and/or combine for best results. If you’re expecting some loss in quality and the end user won’t be watching playback in large streamed content then this or Any Video should work good for you.

Any Video Converter
Link: http://www.any-video-converter.com/products/for_video_free/
Good free product which gets the job done. A little less robust than Super in my opinion, and very similar to Riva as I stated above, but easier to use and probably better for quick youtube edits and uploads.

Adobe Media Encoder
Link: http://www.adobe.com/devnet/flash/quickstart/video_encoder.html
This product does the job pretty well, and I have personally used it for managing some quicktime and .flv video conversions. Visually it is more impressive than the others, but I found overall speed to actually be a bit slower after various testing. There were also some issues on .flv’s that didn’t play audio or video properly after conversion which seemed to work in other editors/converters. Especially interesting in these cases is the videos were output from another Adobe product.. Overall very surprised that Adobe didn’t come out on top with regards to their own platform.

FFmpeg
Link: http://www.ffmpeg.org/
FFmpeg is really at the core of much video conversion on the web, including some of those listed above. If you can master utilizing this tool from command line, or if you’re natively on linux, this is for you. Searching for ffmpeg GUI or frontend will also return some good results if you’re rather not run the commands manually.