I love that Wall-E & Eve statue - it was originally meant to go to one of the Eastern parks (Tokyo, Shanghai, Hong Kong, can't remember which), so glad we got it instead

One of the nice little touches I noticed the first time we stayed in the Santa Fe was there is a decoration featuring a "route 66" style map. Where Anaheim would be, there is a picture of the Disneyland Castle, with Walt Disney himself as one of the punters!
On the family crest on Mr Toad's Diner, it says "No Consumus Froglegus", pig latin for "don't eat frogs legs"!
The retro American car "parked" outside of Annette's Diner has the numberplate "12 04 92", the date which DLRP opened.
I don't know if it counts as a secret, but we were very excited and surprised the first time we discovered the Dragon under the castle. I think that's a really nice touch. We felt the same about the fact you can go upstairs and see the windows, book etc. My wife was used to going to Florida as a child and essentially just walking through he castle there.