It totally depends on what you're planning to do while in town - if you're wanting to focus on the Old Town (downtown) area's offerings - there's this really unique old hotel - The Armstrong Hotel that was renovated some time ago and is totally unique to the area - here's a link to their web site:
http://www.thearmstronghotel.com/If you're looking for something more centrally-located, the Fort Collins Hilton is probably one of the only hotels that's "in the middle".
Or, if you're planning something more toward the south end of town, or plan on going up to Horsetooth Reservoir, there are a LOT of hotels to choose from. I've gotten good recommendations from the Hilton Garden Inn Suites.
