2 different set ups.
The Rocktron ProGap direct out (w/ fixed cab simulator) sounds very very good for very clean or over the top, smashing pumpkins type distortion. In between sounds not so good -- where tube amps are great. It is really like a pre-Pod, Pod. Very quiet too.
I was in a hotel room and all I had was a maxon od, and an art tube mp. I got some good sounds here. Decent overdrive, and overall a little skanky and cutting, which is sometimes a good thing.
. The clean sound wasn't bad either.
As far as doing something with the direct track, there are plug-ins like amplitube and 2 different ones that come with Sonar, Cakewalk's and Alien Connection's (i think). I've gotten into to these a bit. To me they are effects and have been effective at slightly modifying a sound, or making is very radical. But to me, aren't great at recreating perfect, normal guitar parts.
I also use them more on other parts than guitar parts. Samples, drum beats, vocals. I like them for this alot.
Your other option is reamping. Taking the direct signal out of the computer, sending to an amp and micing it. This let's you use different amps/mics/rooms etc. at any time. You need to match levels though, so you need something like
www.reamp.com.