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, a Yoshi appears in the Dark Bloo Inn level. A Ghost Toad owns the Yoshi (Only calling "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. Several other different colored Yoshis can also be found at The Emerald Circus in a cage. If Mario interacts with them, one will swallow Mario and spit him back out crumpled.