Jax Fish House just opened a new outpost in Fort Collins (to go with their existing locations in Boulder and Denver). Assuming the quality stays consistent with the other locations, that's going to be some of the best food in town.
I've enjoyed LaLu's fish tacos in Fort Collins as well - not fancy, but a solid fast-casual lunch with some excellent salsas.
Jax Fish House
928 Pearl Street, Boulder, CO 80302
Jay's Bistro was my favorite place when I was living there a couple years ago. It was the place I would always get my parents to take me when they would visit. I also always enjoyed the Stonehouse Grill. I would just recommend walking around Old Town and there are plenty of good ones there.
135 W Oak Street, Fort Collins, CO 80524