For me VLC plays everything, including transport streams and stays on top so I can play something and still work. For me that should be an option on every video playback app.

Until recently, for anything other than DVDs, Handbrake was useless for me. I used Quicktime Pro to assemble and trim files before converting them. I also use ffmpegX quite extensively due to the vast number of muxing and stream adaptation options.

Although Apple Compressor makes the best looking MPEG2's IMHO.