For me, the fact that the Waves GTR3 Guitar Tool Rack allows stereo setup with two different amps and fx without straining the CPU makes it the most appealing.
I spent all Saturday night comparing demos of some of the guitar sims with a Custom Les Paul into a Daking DI into ProTools LE on a Duo 2x2GHz Intel mac. My primary focus was the sound of the amp sims dry, so I usually turned off all fx. My non-professional impressions were:
Waves GTR3 Software Edition ($380): without the special interface, and only humbuckers, I thought the sims generally sounded pale in mono. Maybe 1/3 of the amps were immediately useable for pop/rock. Using the Guitar Tool Rack in stereo was much closer to the "real thing" than anything else I tried. It was conservative on CPU resources, and the fx were generally better than most other packages. On their own, these sims do not sound as good to me as miking a real cab. In the mix, combined with real guitars, for variety, and for some special circumstances, I do think these are usable in commercial pop/rock (and other) productions. I'll keep my amps, but I'll buy this for variety and flexibility. I found that panning the stereo track narrow still preserved space and sounded much more "real" than the mono tracks.
NI Guitar Rig 3 ($339): I thought had the best sims in mono. If it could do stereo amps, it would be my pick. But it's already hard on CPU; it was the only one that required at least 256 sample buffer. Maybe 2/3 of the dry sounds seemed usable, which is pretty good. All of these sims suffered most with clean sounds, imo, because you can hear the attack of the note, or lack thereof, better than with distorted sounds. I liked that the tuner was integrated into the main window with everything else so I could easily check tuning. It was strange that they had presets mainly for Strat and LP Bridge pickup. This caused the middle position to sound muddy on the presets. Fortunately, tweeking usually solved the problem and cleared up the mud.
Digidesign Eleven LE ($395): I wanted to like this because it was the lightest on CPU and consumed the least screen space when open. I didn't care that it has no fx--I use others anyway. But I thought only maybe 1/4 of the sounds were useable, most struck me as fairly generic, almost like an old POD (I haven't used the newer PODs).
Amplitube LE 1.0x: I don't think it's fair to compare this scaled-down, old version of the software. I thought the sounds were on par maybe with Digi's Eleven.
Marshall JVM410 direct output: all of the sims sounded a little more alive to me than using this output, which I would hope to be the case. This output is okay for quickies, but not for primary tracks on a finished production, imo.
Marshall JVM410>4x12 cab w/Celestion Greenbacks>Royer R121>Daking: Again, I think the attack of the note immediately distinguishes reality from fantasy. The real thing is something like 10% more lively to me--which is a huge compliment to the plugins.
If you put a PSP Vintage Warmer plug on top of them (the "Heavy Rhythm Guitar" preset with the low end rolled down works well), I think any of these programs are useable. I wouldn't want to use any of them without VW, or something like it--maybe the Cranesong Phoenix TDM plugin, or several other alternatives. I used to like only Amp Farm, and even that was just for fun. Since I've sold my TDM system, I plan to replace it with the Waves GTR3.