Several programs that I use all the time. One that I can honestly say has saved my bacon far more then others and if you been reading any film making blogs for any length of time you've heard of it before in the past.
MPEG Streamclip

It's a extremely powerful video and audio converter. Much like Compressor. The one big difference is that it is far faster then compressor. I can't tell you exactly why that may be the case all I can speak from is my personal experience. I am also only speaking about Compressor 3.5 I have not upgraded to compressor 4 so this could be far different for those who have.
Biggest thing for me with Compressor is that is speedy to set up and get compressing or doing transcoding on files. I currently edit mainly in Final Cut Pro (FCP) and I've always found that with FCP you get a better file if I export the sequence at the same codec it was edited in then transcoding to a deliverable format, more often then not H.264
Back when I did a video podcast every week MPEG was what I used to convert everything into the proper MPEG-4 format that the files needed to be so that they would playback on iPods & iPhones. There have even been a few times that I've been able to use it in weird ways.
People often say that VLC is the swiss army knife of playback for me MPEG is my go to format if I can't play something back. There are certain proprietary formats that VLC just for what ever reason can't handle. There have been many times a friend or colleuge can;t deal with a video file and I tell them just to try it in MPEG** and almost always fixes the problem if not I have to put on my DIT harness and go to town.
What programs do you use as your swiss army knife? Let me know.
_**Perian needs to be installed for MPEG to be most effective._