I've only ever messed around with it in 3D Software - there are plugins in After Effects to do it, not sure if there are any photoshop plugins to help translate the depth order to 3D depth.
I loved the whole 3D section of the Black Dossier, which I think worked well.
So which strips would work especially well in 3D?
Dredd, obviously.
Stront - could do some nice effects with the electronux, time bombs etc.
ABC Warriors - Langley could look quite epic in 3D
Shakara - I can't imagine what Henry Flint in 3D would be like...