I use Native Instruments Guitar Rig 2 which is kind of pricey but hands down, the most versitile and best sounding of all the amp simulator programs.

I use a hand made all tube pre amp that feeds my guitar into the computer and then it is processed by Guitar rig.

I also record with real tube amps also using a Palmer PGA-04 speaker simulator

What an awesome piece of gear the Palmer unit is. I saw that Satriani had recorded a bunch of stuff using it and so I checked it out.

Here's a link to some Guitar Rig sound clips.
Guitar Rig sound clips