When we planned our trip, I dug through the threads here to find out about characters, I saved the tips and here is what I came up with: (sorry to whoever originally provided these tips for not giving credit.

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Universal Studios
Character Tips:
Lots of people seem to miss Shrek. He is found in the alley between the Shrek building and Monsters Cafe building. He is there with Donkey.
Some other characters are also found here. The Cat in the Hat characters are in Suessville. Rugrats and other characters are found outside the Lucy building.
US:
Scooby Doo and Shaggy, Woody Woodpecker, the Rugrats(Tommy, Chucky , Angelica), Eliza Thornberry, Spongebob, Jimmy Neutron, Donkey, Shrek and Fiona, the Flintstones (Fred, Wilma, Barney, Betty), Doc Brown, Marilyn Monroe, Curious George and the Man in the Yellow Hat, Crash Bandicoot
**Spongebob gets his own area in the back of the Nick store (where the Jimmy Neutron ride kicks out). You get your photo done if front of a Bikini Bottom back drop. We also found Dora outside this store.
IOA:
Spider-Man, Captain American, Storm, Rogue, Wolverine, Dudley Do-Right, Popeye, Bluto, Olive Oyl, Betty Boop, Woody Woodpecker, Cat in the Hat, Thing 1 & Thing 2, Merlin, Sam I Am, the Grinch.
Most of the characters from Nick can be found by the I love Lucy store and the scooby doo Chracters also do a stage show bit outside ET.
Shrek (and sometimes Fiona) can be seen opposite where the Shrek show kicks out. with Donkey.