I don't remember which museum ships I visited, but I do remember going on an American SSN. I don't remember which one. She was nested alongside a tender at Point Loma some 50 years ago and I went with an enlisted technician to get something from the tender. We saw the nuke alongside and just went across and climbed inside. We took a leisurely stroll from the after hatch going forward. After we passed the midships section the duty officer spotted us and called out. He was in his skivvies. We ignored his order to stop, climbed up the ladder forward, and headed for home. He was obviously too embarrassed to come topside and chase us as he was not wearing a uniform.

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I can remember visiting the following subs:
Cavalla (twice - once in the 1960s while still active - and now in Galveston)
Cobia (Manitowoc)
Silversides (Muskegon)
Croaker (Buffalo)
Nautilus (Groton)
Growler (New York)
Dolphin (San Diego)
B-39 (San Diego - Russian Foxtrot - what a hunk of junk)
U-505 (Chicago)
Trieste II (Keyport)
Maybe I'm forgetting some. I've seen others from a distance, like the Pampanito in SF and a Russian Juliet (in Helsinki!), but didn't manage to get a tour.
How many have you been on?