I believe Tony Hawks underground asked you to set time in some of the later versions but it was accelerated time for game dependent events, not RTC as found in pokemon and such.
There was a yoshi game that also had motion sensor, nothing else springs to mind though.
The only other thing of note is the EEPROM patches required by the classic nes, dragonball z and some other dragonball titles. NES stuff should not be worried about as HVCA and pocketnes surpass it and dragon ball games are a)bad (even as licensed titles go) and b) got patches.
Hmm... I'm not sure but I think Pokemon Pinball Ruby/Sapphire come with a rumble pack. I'm just assuming this because the old Pokemon Pinball for the Gameboy Color had this. I have no idea though.