I generally use Edmunds.com for most anything car-related, and I think they use Autotrader.com -- you could give that a spin.

Regarding manual and diesel, I know you can find manual transmission cars, but yeah there are probably some models that don't even offer a manual. For diesel, the availability at gas stations is reasonable, but I'm not sure you'll find many diesel cars. Maybe a handfull? I'm actually kind of curious about your results with that. Other than the random old Mercedes and some pickups, it's just not the type of thing you ever see on the road.

Then again, I know precious little about the recent developments in automobiles. I just buy a shitty old used car about once every 5 years and then stop paying attention.