One simple and fast way once you have the master avi, si Freemake. Its pretty darn fast and free too :). I just wish it supported image sequences as input. Oter than that, h.264 straight out of AFX or premiere gives good results here after fiddling with settings, but maybe not for longer clips. If you want top notch encoding tips, you need to seek out the shady part of the movie release scene on the interwebs, aka the pirates 
Personally I’d dump the whole quicktime stuff. Nasty software from an even nastier corporation, and completely unnecessary today. Last time Quicktime was relevant was back in the mid 90’s.