1) I checked the intro but wasn't able to hear one single note of the theme. Did you really mean the video with Millenium Star falling in Peach's garden?
Yea, during the part where the Millenium STar makes his appearance. I'll plug up my N64 and see if I can time it and give an exact timing of when to listen.. :)
.. and here's a few more I thought of.. :D
-Super Mario Bros 3
(Music Box music that makes the Hammer Bros on maps fall asleep)
-Mario Party 2
(Mystery Land Board has a couple of the bars floating around in it)
-Paper Mario
(when you turn yourself into 8-bit by dropping into a pot in one of the rooms of the Haunted House)
-Paper Mario 2
(can be heard during regular battles [someone else has already mentioned this])
(when you turn yourself into 8-bit by dropping through the celing in the Moon Base)
(a remix is heard at the beginning of every chapter [I think someone else has already said this one, too])