In Paper Mario, you would find the species on an island where they would have their own village. Your goal here was to go out and save a bunch of Yoshi children, and would also gain the help of Sushie. In Paper Mario: The Thousand-Year Door, there is sometimes a Yoshi on the Excess Express, but the only prominent Yoshi is the Yoshi Kid, but his Stampede attack calls in a small herd of other, normal Yoshis to trample the enemy.
In "Paper Mario Color Splash" Yoshi appears in the "Dark Bloo Inn" level. A ghost Toad owns "It" and Mario has to get it back from the "Shy Guy" after battling a "Shady Sledge Bro". When Mario returns "It" to the room it came from and paints it, it's revealed to be a "Yoshi". Mario can try to ride him but, he runs away before he can successfully mount on him.