For me, it depends on the project. I'm doing a Judy Niemeyer Paper-Pieced quilt right now. I use the 28mm for accurate, 1 or 2 layer cuts or trimming up the finished block. The 28mm is great for freehand cutting around curves. When I'm cutting 12 layers of template pieces, I want the 60mm with a new blade.
My normal go to cutter for up to 6 layers, is my 45mm. I guess you could say it is my favorite. I wouldn't give up any of my rotary cutter sizes. I have duplicates of all my cutters. If I go to a class or sew-in, I have my travel box packed with all 3 sizes and extra blades.