I'm a big fan of Amplitube and Guitar Rig sims (but to be honest, i haven't tried many others).
Amplitube excels at simulating specific amps. If you want that '65 Fender Twin or Marshall JCM800, that's what you get. It's very straightforward and simple. They're licensed to Fender, Orange, Ampeg, and others, so they have to be great recreations.
Guitar Rig doesn't seem to mimic specific amplifiers as proficiently, but I use GR when I want a more complicated setup. You can drop in their "marshall sim", split the signal and send one line through a noise gate, which then routes to a different amp, which then splits again and has the upper frequencies panned Left and the lower frequencies panned right, with separate Delays on each.*
I also have a Boss GR-10 around somewhere, but since I have these sims I never really use it. I've also got a Line6 Spider amp which I could use to hard-code the sound, but the flexibility of the software wins every time.
* I've never actually tried this, I just made it up as an example.