There are many references in Paper Mario TTYD, and I'll list some of them!
Remember Petalburg City The place where Koops used to live Petalburg City is a name of a town in Pokemon Emerald.
In the Glitz Pit when you fight Rawk Hawk for the first time, one of the people in the audience shout "Jumpman!! Wait, who". Jumpman is the name of Mario in the game Donkey Kong.
Sometime after you ride the train to Poshley Heights, you'll receive a message from the real Zip Toad. If you look closely, Jr. Troopa from the first Paper Mario is flying outside the window.
After you defeat the Shdow Queen, go back to Poshley Heights. Go to the outside of the place where you got the 7th Crystal Star. Next to the fountain are Bow and Bootler from the first Paper Mario.