I suggest The Press - unpretentious, frequented by professors, students and locals, with the mellow of a campus coffeehouse but more upscale...some unusual menu items - they do great things with eggplant, mushrooms, and salad combinations.
Zikes, how could I forget Walter's (on Yale). Eclectic menu with pages of salads, sandwiches, specialties with Indian, Persian selections...also Afghani fries (pouffy, lightly battered rounds of potatoes that, not sure why, but are hopelessly addictive when eaten with the chimichurri-like sauce they bring to dip them in...). I actually like breakfast items the best-really good omelets.
It's been awhile since I've been out that way, but Full of Life, a French bakery/cafe on Bonita, had fantastic sandwiches, soups and baked goods. If you want something more upscale, I always thought that Tutti Mangia far surpassed Aruffo's and Harvard Square. If you have time, head up to 21 Choices, in the Ralph's shopping center at the corner of Foothill and Mountain, for the best frozen yogurt.
I loved Full of Life, but heard that they've changed owners and aren't particulary good anymore.
Tutti Mangia is much better, but also much more expensive. I totally forgot about them! And don't forget you can also get 21 Choices in Oldtown Pasadena, if that sways your choice making in any way.
Saca's Mediterranean Grill has some great falafel.
Some Crust has delicious cookies and cakes, but I don't know how the cafe next door is.
Don't forget to get some peppermint ice cream at Burt & Rocky's!
If you want fancier, Harvard Square has a salad with baked brie that's pretty good.
Aruffo's food is mediocre in general but the warm bread stuffed with fresh tomatoes that you get before your meal makes everything worth it.
Claremont Juice Co. has a huge variety of sandwiches (I like roast beef), fresh squeezed juice, and tons of different smoothies (some named after the Colleges--like a Pitzer Colada or others equally cheesy)