You are using WAY OVERKILL on the bitrate. You can't see the difference above 800kbps for SD adn 1000kbps for HD. Anything more is a waste of space.
I disagree with this. I personally use 1200-1800 Kbps for SD (1200 for H.264, 1800 for MPEG-4), and 4Mbps to 6Mbps H.264 for HD content. Then again, my encodes tend to stomp all over SciFi and Comedy Central's encodes for TV shows in quality.
If you think 1Mbps is enough for HD, think again, I can show you two 720p encodes for Fifth Element, one at 2.6Mbps and another at 4.4Mbps, where the 2.6Mbps encode has obvious visual artifacts not present from the source Blu-Ray disc. Flat colors, details wiped away by un-natural looking gradients on Willis' forehead... A bunch of things that are noticably wrong, but at least H.264 isn't really blocky (unless you look at the background a lot).
Big mistake encodeing above iPod maximums. In future you will regret it cause none of your work will be portable. You may not care now, but in future either you will or your kids or their kids will.
more than 640 wide is not wise.
This I agree with. As things move more towards HD in the future, why throw away the SD encodes when they can be your portable copy?