(An Olympics-inspired competition.)
The top honor in this category is really no contest: Rensselaer Polytechnic Institute walks away with the gold. Even when you have it right, it looks wrong.
There are a number of solid contenders for the silver and bronze medals. I like Duquesne for the silver: the disparity between how it's pronounced and how it's spelled makes for a high degree of difficulty, as they say in gymnastics. This is one of those names you could spend your whole life hearing and saying and yet not recognize when you see it on the page.
But there are a few others giving Duquesne a run for its money: Bryn Mawr, of course, and dark horse competitor Bowdoin. Don't count either of those schools out just yet. And I think you also have to consider performance in tallying the final scores: Johns Hopkins is not difficult to spell, but it is nevertheless frequently misspelled. Could that put it in the top five?
(Embarrassing admission: I personally have trouble with Stanford, the selective West-Coast university. I want it to be "Stamford," like the city in Connecticut. I don't know how widespread this problem is, though.)
I think there should be a separate category for colleges whose names bug me. Wesleyan is a big one. Also Tufts.
Your turn! Have I overlooked your favorite? Should your alma mater be on the list? Please help me out. I have a mild case of the flu, and this is as deep as my thoughts can go right now.