IoA: main store (it will get crowded with people hiding from the rain, but it is a large store with a lot to look at)
across the "street" from the main store is a candy shop and Christmas shop; they are open to each other inside, so lots to browse (they sell Big Pink donuts too...that's where we grab one before heading out of IoA)
Jurassic Park Discovery Center...upper floor has a burger place to eat, lower floor is the Discovery Center...lots of neat interactive things, if your crew is into dinos
Poisidon's Fury show or Sinbad's show (if the times line up that you can go inside to wait)
If you don't have Express Pass:
Cat in the Hat ride
Forbidden Journey
Spider-Man
Hulk
all rides that can have long waits, mostly, if not all inside lines (with Express Passes, the lines may be rather short, so beware)
US:
Minions ride (two inside pre-shows, ride, and shop are under roof (EP line is mostly under cover, not sure about regular line)
Shrek, ditto of Minions
Mummy line & ride is inside, although with Express, it might not be a long wait
Men In Black (inside line and ride...again, may not be long)
Fallon ride (pretty sure wait & ride is all indoors...never seen it)
Simpsons ride, mostly under cover for the line, pre-show/wait and ride is all indoors
ET (line under cover, pre-shows, and ride inside)
If you are there at show times, Fear Factor and Animal Actors are open, with an overhead cover...Terminator and Horror Make-Up are inside. (You can walk around inside Horror Make-Up & look at items, without going to the show, or while waiting for the show.
There's also several places to eat in both parks. We like to go to Finnegans...if the rain lets up & you are by a window on the one side, you can watch the Blues Brothers from your table.
I'm sure there's more, but I'm going from the top of my head
