I understand exactly what you mean. When I first was buying them when I'd hit a sale, I'd just buy what caught my eye and not paying attention to what went together. So I was in the same boat.
What I did was cut them all up into squares and strips and made scrappy quilts. I still have a few that I really like but can't figure out what it goes with so, I just decorate with them.. a nice basket with pretty fat quarters is very pretty.