1. Abstract Art (Earthbound)
I don't think ever laughed so hard on encountering an enemy before or since this, although Earthbound has a lot of strange and hilarious enemies. There is nothing more enjoyable than battling a painting in a false reality.
2. Master NORG (Final Fantasy VIII)
Bujurururu! NORG is a sudden revelation, hidden away in the school basement, belligerent and waving huge yellow hands around. He is both humorous and terrifying (backed up by the spooky organ music that plays when you meet him). Kinda reminds me of some of the stuff from Parasite Eve, but definitely lighter in tone.
3. Lesser Dog (Undertale)
As a big fan of all the Earthbound enemies, it was inevitable that I would love all the creative Undertale enemies too. I chose the Lesser Dog because that endless petting is just excellent and good.
4. Darkside Heartless (Kingdom Hearts)
I love the atmosphere Kingdom Hearts managed to create within a cartoonish world full of Disney characters - there's a lot of good use of shadows and clouds and spooky things throughout the game. There are many different kinds of Heartless, but I like this one a lot because it is so imposing, and a great introduction to the game's enemies. Also I just like those times when I get to jump onto an enemy's shoulder.
5. Ram (Spyro the Dragon)
Finally, we end this list of fearsome foes with the most terrifying of them all, the ram from the Stone Hill area of Spyro the Dragon's first world. Fear him.
Special bonus mentions: Bowser (Super Mario Bros. series), that evil tree that eats you in Misty Bog (Spyro the Dragon), Temmie (Undertale), that one Sudowoodo (Pokémon Gold/Silver/Crystal), Hell House (Final Fantasy VII).