A few I consider ugly...
The Colt 2000. Who in the HECK on the Colt board of directors looked at drawings of that thing and said, "Yeah, the public will buy this."? Would it have been too hard to go to a few gun ranges, show regular shooters pictures of that gun and ask them if they'd buy it?
The Colt Double Eagle. Take the aesthetic of an M1911...but mix it with the ugliness of a Ruger P90 from the slide down.
Which brings me to the Ruger semi-autos. Yep. Ugly.
The Smith and Wesson Sigma. My God. A polymer gun that makes Glocks look good in comparison. About the only polymer gun uglier than the Sigma would be those EAA polymer framed things I can't remember the name to right now.
That being said, I'd have to vote for the best looking semi-auto as being the Luger in all it's various incantations. Still the belle of the ball in the looks department.