I didn't read this whole thread, so I bet some of this stuff has already been mentioned, but here are some things we noticed/I found out online...
-At the Indiana Jones ride, apparently you can ask a cast member for a decoder card for the "Marabic" inscriptions throughout the queue area and the actual ride. They used to give these cards to everyone but they stopped because they were getting thrown all over the park or something like that... We haven't confirmed this, but it sounds pretty cool.
-There are a bunch of animals on Thunder Mountain that we only just noticed the last time we rode it. Possums, skunks, snakes, you don't notice them a lot of the time because you go by so fast.
-Under the gate to the castle to the main Fantasyland entrance, there's a small gold circle about the size of a penny on the ground. This marks the exact center of the park.
-And finally, this is just something that applies to any roller coaster, but during the loop on California Screamin, turn your head to the side. It's seriously the coolest thing ever, Paradise Pier just flips around.
That's all I can think of at the moment. I'm actually making a small journal of some of these stuff so I won't forget any of it when we go again in the spring.