A character stands out as ugly when the other characters are not. For that reason, the Bean Seller in Ocarina of Time immediately jumped to mind when you asked about ugly characters - and he's eating all the beans!
http://zeldawiki.org/Bean_Seller Professor (of the undead?) watch me dive!
[url=http://zeldawiki.org/File:Mizumi.png]http://zeldawiki.org/File:Mizumi.png[/url]
If you looked like this, you'd be depressed too
[url=http://zeldawiki.org/File:Grog_MM.png]http://zeldawiki.org/File:Grog_MM.png[/url]
The Great Fairy is pretty much nightmare fuel too
[url=http://zeldawiki.org/File:MM_GreatFairyClockTown.png]http://zeldawiki.org/File:MM_GreatFairyClockTown.png[/url]
Is it a he? Is it a she? Oh forget all that and kiss me, you crazy adventurer! LOL
[url=http://zeldawiki.org/File:Goron-elder.png]http://zeldawiki.org/File:Goron-elder.png[/url]
Then there's Falbi of Twilight Princess (bet you put this horror from your memory - and I don't blame you!)
[url=http://zeldawiki.org/File:Falbi.png]http://zeldawiki.org/File:Falbi.png[/url]
and Ooccoo (You can KEEP your eggs. *shudder*)
[url=http://zeldawiki.org/File:Ooccoo.png]http://zeldawiki.org/File:Ooccoo.png[/url]
Gully from Skyward Sword is also ...memorable
http://zeldawiki.org/Gully My daughter recommends Master Xehanort from Kingdom Hearts
http://fc00.deviantart.net/fs71/f/2012/275/0/f/master_xehanort_by_uxianxiii-d5gmehh.jpg Remember Don Corneo of FFVII? He wanted to snuggle...
http://static3.wikia.nocookie.net/__cb20120103180003/finalfantasy/images/e/e7/DonCorneo-ffvii-field.png Then we remembered Ozzie & Slash from Chronotrigger
http://chrono.wikia.com/wiki/Slash http://chrono.wikia.com/wiki/Ozzie