I've been playing a lot lately with my pedal board into guitar rig 3. It has built in pedals, but its not very handy to do switching mid song. Frankly I almost enjoy my analog pedals better than most of the built in pedals (the tubescreamer sounds great but the others are okay). They also seem to respond and sound much like they do through my blues junior. I continue to be impressed by guitar rig.
Does Guitar Rig 3 take pedals? You tell me...
I also have a video of these same pedals running into a Fender Blues Junior if you want to compare the real thing (sorta)... Enjoy!