Personally I've always liked the Munch Mammut, especially that 2000 with the purple bodywork and giant quarter fairing.
As far as ugly motorcycles... I'd have to go with BMW. Not all of them. I've always liked their GS1200 adventure bikes, and I really like the new GS310 naked bike they came out with last year(especially the white w/red&blue). There were a couple others that looked ok, but so many of them just looked horrible.
Harley has a lot of ugly bikes, some of them look perfectly fine. I really like the look of those blacked out sportsters. Only problem is I can't stand the thought of owning a bike that comes with a mandatory dress code involving bandanas and nothing but HD tshirts, a smug attitude, and a new bike price tag on something that remains unchanged since 1975.
I find it interesting that most of the bikes popping up here are older bikes. I agree that I've looked at plenty of them in the past and thought they looked horrible. I do notice that the older they get, the more willing I am to accept their styling and appreciate them for what they are. At the same time. I think most newer bikes, especially sportbikes, just keep getting uglier and uglier... I think there was a point where sportbikes looked gorgeous, 1997 GSXR750 in black/red, 1998 R6 in red/black/pearl white, 2003CBR600RR, all amazing looking bikes. Then you hit the mid 2000s when everything started going downhill when they started forcing too many angular designs(at a time when all of the motogp bikes were all still nice and curved, so clearly they knew what a fast bike should look like), with things like goofy headlights like that 2007 Yamaha R1, BMW S1000rr with it's mismatched headlights and fishgills in the side fairings. Kawasaki just went off the rails after their 2003-2004 zx6r and 2004-2005 zx10r, both of which looked great, but then have been replaced with nothing but awkward looking bikes.
Either way, all the newer bikes being so ugly makes it that much easier to not be interested in them, on top of the price tags, and unnecessary/overbearing electronics that come on bikes now. Pretty much all of the bikes I really like are still from right around that 2000 time period, which is great when it comes to finding stuff cheap on craigslist. Two exceptions for great looking newer bikes... Indian Scout, and the KTM Superduke 1290r.... dreamboats.