I would have to say that Cyclohm is my favorite. For one, Cyclohm is the C.A.P. mon that first grabbed my attention and drew me in to the C.A.P. project in the first place. The sprites were well-done and the design itself screamed awesomeness.
Pretty much all of the others would have to tie in as close seconds to Cyclohm: they all are made of awesomeness and each have qualities about them that seperate them not only from official Pokemon, but from one-another as well. Some have type combinations that (so far) do not exist among the official Pokemon and pull off those typing combinations well. Pretty much all of them have unique designs that you can't help but fall in love with, ranging from kick-ass awesome to adorable.
Colosoil, of course, holds a special place in my heart as well since this was the first C.A.P. mon I've participated in the creation of.