Lots of speculation, so I decided to do some some tests on the sequencer performance:
Global Prefetch set to 30frames, 4096MB of cache, AVI JPEG 50% quality: 2m28s
+ UI Locked and no image Display: 2m28s
+ Sound track caching, MPEG seek per-track set to 60 rather than 25: 2m28s
+ Immediate re-render, to test for effect of disk caching: 2m28s
Conclusion 1: Surprisingly, none of the performance-enhancing options seems to do anything.
Same setting as above, AVI JPEG: 2m28s
+ Encoding set to Quicktime H264 @ 50% quality: 4m08s
+ Quicktime H264 @ 75% quality: 4m02s
+ Quicktime H264 @ 95% quality: 4m11s
+ Encoding set to FFMPEG H264, H264 Preset @ 600kbit: 8m18s
+ Encoding set to AVI RAW: 1m58s
Conclusion 2: The encoding engine makes a huge difference in speed. AVI RAW is the fastest if you have the disk speed to back it up. FFMPEG H264 is the slowest.
+ With antialiasing, AVI RAW: 1m58s
+ without antialiasing, AVI RAW: 1m18s
Conclusion 3: Antialiasing makes a difference, but the quality loss is huge, especially when all the input clips have different resolution.
Scene used: 2000 frame long sequencer with 6 different 720p MPEG4 video input, 3 1080p PNG sequence inputs, dozens of images, dozens of transitions, 1 audio track. Output is 720p with Antialiasing.
Test Methodology: System is restarted after each test, so the effect of disk cache is minimal.
Test system: 2.2Ghz i7 Macbook Pro, 8GB RAM, Radeon HD6750, 500GB SSD