Here's another vote for the Nero encoder. It works all the way up to HD resolutions and the quality is top notch.

What container format does the nero encoder output in for h.264, quicktime mov, mp4, or old avi?

I realized I actually have the nero suite and just tried to use nero recode to make a h.264. It came out as an .mp4 which is alright but it resized my video for no apparent reason to something like 1156 wide instead of 1280 wide like it should have been, did the same for height but don't remember the new one.

You just need to play with the GUI a bit more. There are a couple of templates with pre-set sizes, but you aren't limited to them. I'm sure it will do exactly what you need it to do, and the process is easy once you figure out their mindset.

If you don't have version 7 yet, the upgrade price is quite reasonable and IMO it's worth it. It will now convert a file directly from either a clip or directly from a DVD for instance.
This is really cool combined with Slysoft's AnyDVD, a program which removes annoying things like copy protection, zones, and promos before the movie (if you choose that option). With AnyDVD installed, you can make an mp4 directly from any DVD (just for your own personal backup of course)! It works well with NLE output files as well. I have used it successfully with both M2T files and Cineform codec avis.