I can think of a few, but I'll start by saying you were a fool to underestimate a necropolis where the most powerful unit is Skeleton Archers. They are the crux of the Necropolis' units. If you have strong necromancy skills all you need is Skeles and Vampires.
So, times where I underestimated my opponent and lost horribly...
Well I'll start with the recent case of this were I was playing Dissidia and I had to fight Chaos for the first time. My Zidane was a good 20 levels higher than him so I thought, hey, I'm going to totally murk the boss of this game... nope. I did it only after a helluva lot of practice.
I underestimated the boss of chapter 1 of the first Neverwinter Nights, I forget his name but it took me a good long while to finally trump him.
There's a famous case of underestimation with the first fight with Seymour in Final Fantasy X. I think a lot of people have the idea where they're all like, "There's no way this guy's tough, I'm gonna destroy him", then, BAM!, Anima.
Other than that? The first time I underestimated High Templar when I had Carriers was a big mistake.