x264 encoder will get you very good quality in a small filesize today. Each encoder does different things to optimize where the bits are spent, so run tests on your material with different encoders.
You'll find the h264 encoder one bundled with Quicktime Pro to be least efficent, while you'll find x264 to be the most efficent, with most of the encoders falling somewhere inbetween.
If this is your final master deliverable that needs to stand the test of time spend the extra time, getting an uncompressed file out of your NLE, and run that through x264 into an .mp4 container.
If this is just a proxy for review, just export whatever is quick out of your NLE.