One thing you have to remember about NIN is that trent does a LOT of sound processing on his computer. Because of this, a lot of the things he does to his guitar sound can't necessarily be duplicated in real time, at least not with any commercially available effects that I know of. I'm working on a homemade box right now that intentionally undersamples a signal in order to get a really ugly, deconstructed guitar sound. Another trick he uses from time to time is pitch shifting. If you try to shift the pitch of a signal without changing its speed, you have to add new information to the signal to keep the speed right. Since this new information comes from a computer algorhthym instead of an actual instrument, this means that the further you shift the pitch, the less it sounds like whatever made the sound originally. You can try this out with any effects processor that lets you do pitch shifting. Unfortunately, most canned pitchshifters only work well with single notes. Sound forge also has an algorhthm that lets you do pitch shifting. The single note thing isn't a problem there, but then once again your stuck with something you cant do in real time.
Oh, and as to the pod, i've never used one, but line6's web site says trent uses it, so drstawl is probably on to something there.
Whew! sorry about the long winded response, but as you can see this is something of an obsession of mine ...
-Nate K