I love Pearl Jam more than AIC. However, I think AIC takes the cake as the more "original" band. I do believe Pearl Jam has some amazing songs, but many fall into the more adult, or catchy (for commercial purposes) side.
As for acoustic PJ songs that are as good as AIC's i have: Footsteps, Elderly Woman Behind the Counter in a Small Town, Fatal, Off He Goes, etc... Of course, none of these come even close to Nutshell, except Off He Goes, which is just as good.
PJ songs Opeth should cover:
I Got Id <--- wooo just thiking about it makes me happy!
Sleight of Hand
Nothing as it seems
Oceans
Tremor Christ
Parachutes (i think this could be funny, but interesting)
Low Light (what Mike (Akerfedlt, not McCready) could do with that little solo in the bridge would be amazing!)
Blood (with growls)
Hell yeah... we need PJ covers!!!