What are the best apartments for students in Fort Collins?

That depends on what you're looking for. If it's proximity to campus these new apartment buildings are leasing now.
The Summit on College south of Prospect http://www.thesummitoncollege.com/.
Another new complex that's close to campus is The Grove on Rolland Moore Drive http://www.gogrove.com/locationdata.asp?loc=46

Did you know there's special financing for students who buy with their parent's as co-signers? Look into "kiddie condo" FHA loans, with low down payments (only 3.5% ) and competitive interest rates. In an appreciating market such as our right now, and after the tax savings of owing, you might actually make money.