An amazing SLR body, manual focus: Contax RX. Gorgeous, well-built. Integrated winder. Great lenses. Feels like a real camera.
AF: I love my F100. I had an F6 for a while, and it IS better. But, unless you have both in-hand at the same time, you'll likely not feel that the F100 is lacking in any way. I don't miss the F6 at all now. The F100 may even be 'better' in one important aspect. It's not nearly so precious. I'll stick it in a beach bag and not worry. The F6 i always wanted to keep pristine, and having that LCD on the back just made me need/want to handle it a bit more gingerly. Both are built 'tough,' of course.
I still have an EOS 3. It's still fantastic, although i don't love the way it looks. But, it still uses the best AF lenses. 35L, 50L or 1.4, 85L or 1.8, 135L —*all amazing.
All that said, the camera i am most in love with at the moment is the Nikon FE2. Feels more like 'photography' than the F100 or EOS. More like what a Leica M felt like, except with a viewfinder i actually LIKE. With a 50mm/1.8 Series E on it, it's as small as the M7 or Ikon i used to have, and i like that little $50 lens as much or more than any Leica lens i've owned.
I had an F4 for a while, too. Nice, but maybe a bit too big? I think i got one after having an F100, but only because i wanted to try the waistlevel finder. That experiment didn't prove to be as valuable as i had hoped, though.
[Oops — i got so involved in the reminiscing that i forgot this was supposed to be about AF cams.... Sorry.]