Penn is just called Penn.
SUNY (State Univeristy of New York) is said "Soo-nee."
I've also heard CUNY (City University of New York) is said "koo-nee" (rhymes with Rosemary or George Clooney).
In fact, SUNY Albany was SUNYA, and was sometimes called "soon-yia" (like the name "Tanya") although more often "soo-nee A."
Univerisy of Texas at El Paso is called "you-tep" (UTEP).
I'm sure there are others.