No clue on how accurate this list is as of today but here you go;
http://en.wikipedia.org/wiki/List_of_submarine_museums
I've only paid visit to U-995 in Laboe and it was a nice tour. There's also a Marine Memorial in Laboe well worth a visit.
Unfortunately I had no time for U-2540 in Bremerhaven but I'll be sure not to miss it next time.
And if i ever visit the U.S I sure won't miss a tour on a Gato or Balao.