I'd use Compressor to create the h.264 file you need. Same frame rate as source. AAC audio at 44.1kHz. Video dimensions really depend on where it's going. For Vimeo, keep it at its native resolution. If you are building it into your own website, you can reduce the frame size.
My practice is to always export a self contained movie with 'current settings'. Then I use that master file for compression to web or DVD...etc. Finally I archive the self contained quicktime for future use.
C2V is right, h.264 is your cleanest, highest quality, lowest bit rate option. Generally for a website, I use compressor, 720x405, bitrate of about 1200, add about 25 on the detail frame controls, two pass VBR.