I just started grad school at Cornell after finishing my undergrad at Penn State, so I have some experience with Ithaca and a lot of experience with State College (I actually lived in State College before undergrad, so I know the area very well).
State College is a great town. It's one of those towns that is just the right size to have some nice amenities without the typical urban problems. Good public transit, a few quality restaurants, bars ranging from undergrad dives to classy, etc.
As the other poster said, State College has a great running scene. Miles and miles of trails and bike paths. Lots of runner safe streets as well (this is important when there is snow on the trails and bike paths). There are some good running groups as well.
Having lived in State College for 24 years, I could go on for hours. I don't want to ramble too much, so if you have anything specific you want to know about, go ahead and post it and I'll elaborate.
Penn State itself is a good school. I think it's underrated by many, but it really is a top notch academic institution.
As for Ithaca, it has been nice so far. I haven't found the great running locations yet, but I haven't been running more than 30 mpw since I moved in. Once I get back in shape and start running I might find some good trails. What I said about State College having solid amenities without urban problems applies to some extent with Ithaca as well, however State College is much more affluent than Ithaca.
Just looking at the towns themselves, I'd lean toward State College, but that might just reflect my hometown bias. Ithaca is Beautiful and is a nice town as well. I guess I would say that you can't go wrong with either.
Again, I don't want to ramble too much, but feel free to ask if there is anything specific that you want to know about or anything you want me to compare between the two towns.