Thankfully there aren't many pedals that are shockingly un-handsome but i have personally swayed away from buying a fair few EHX pedals because of looks, for fear of upsetting the zen and colour scheme of my board etc.
Some of Wampler's pedals and colour schemes aren't too sympathetic visually but sound amazing.
Ditto; some of the Fulltone range look a bit naff. Xotics pedals are mad with the comic sans font but they do have a charm that makes them a keeper.
Some pedals have been taken off my board entirely for colour reasons. Anything yellow or orange generally. Shocking electronic gadgetry based racism there I admit.
Are you a tools of the trade, i.e. its all about the sound, kind of person?
Or is your rig equally a piece of art to be savoured?