I spoke to my sister who's lived there for 30 years and asked where she liked to eat that also had a good wine list. After she mentioned that Olive Garden and Melting Pot sold the most wine in town, I asked for her recommendation of places that might be owned by chefs or local families and that aren't chains.
Jay's Bistro was mentioned as where you go for fancy food and wine "but it's expensive." YMMV.
Domenic's Bistro & Wine Bar also has a good reputation in town, but they don't put their wine list on the website so who knows what' they've got? They do mention that their selection is "refined", so make of that what you will.
Cafe Vino looks like the place you'd stand the best chance of getting a good bottle of wine. "Coffee by day, Wine by night" they say, a theme continued by Genoa Espresso & Wine , who seems to have a pretty good list of locally-brewed beers.
I haven't eaten in any of these places lately, but these are the classy joints at least one local recommended.
-Eden (lots of terrific craft beer being produced in Fort Collins these days, so you might avail yourself of the opportunity to enjoy some in situ)