Hidden Gems

Mainly aimed at kids, so not the likes of Waltz With Bashir (brilliant as it is).
 
For me, The Little Match Girl (Disney version)
Rescuers Down Under (those eagle flight scenes.. wow, a highly underrated film IMO, I think a lot of people were put off by the first) 
The Secret of Nymh
The Prince of Eygypt
 
 
Oh and The Great Mouse Dective,  screw you all, I love it.

@bruno0091 said:

"Oh and The Great Mouse Dective,  screw you all, I love it. "

I wasn't aware people hated it? Personally it's one of my favourite Disney films.

@bruno0091: Not familiar with a few of those, but The Prince of Egypt and The Great Mouse Detective were great!

Great Mouse Detective, though I haven't seen it in a real long time, is my favourite classic animated Disney movie.

The Iron Giant. 

The Secret of Kells was quite good. It was nominated for Best Animated Feature last year (aka the 'runners up to Pixar' award) and it's now on Netlix streaming. It tells a medieval Irish folk tale with art inspired by illuminated manuscripts. Check it out!

Hmm, I'd need to think about it a bit. I admit to liking An American Tail a lot when I was growing up, but that's not really that obscure.

I saw The Secret of Kells a while back and fell in love with it pretty much immediately. I think it's streaming on netflix, and you should all take it upon yourselves to see it. The animation is stunning.

The Last Unicorn!!!! That movie kicks all varieties of ass!

The animated version of 'Watership Down' is pretty good, and quite violent for what is ostensibly a children's story

@Pickle said:

" The Iron Giant.  "

Good pick!   
 
How about Titan A.E.?  I thought it was a pretty good sci-fi action animated movie and it had Drew Barrymore as a voice actor. It's one of the few straight-up action animated movies I can remember seeing that was made in the West.   Disney did something similar later with Treasure Planet, but it wasn't as good.  It did have a better title song though  by John Rzeznik (Goo Goo Dolls).
 
For something weirder, but still worth while there are a few more like Allegro Non Troppo and Fantastic Planet.  The former is a darker version of Disney's Fantasia and the latter is well, just plain odd.  It's about some alien world where human-like people live in fear of the giant blue people who also reside there.  I'm not saying it's good, I'm only mentioning it because it is quite unlike anything I've ever seen and I watch a lot of crazy animation.  Come to think of it, Light Years (Gandahar) is a bit like it.  Those crazy French!  I guess I could mention Interstella 5555, the Daft Punk movie, although that might be more of an anime or hour long music video.  I wonder why Gorillaz never made a movie?  I still think they should.  
 
There were a couple of Heavy Metal movies made, but I didn't think much of either of them (Heavy Metal & Heavy Metal 2000).  When it came to that more adult content, I think I preferred Ralph Bakshi's Fire and Ice or Wizards.  Of course, there is Lord of the Rings, too but I don't think that's all that "forgotten" these days (it's now on Blu-Ray). 
 
If you want something really forgotten, there is Starchaser: The Legend of Orin, Flight of the Dragons and Time Masters.  I remember seeing the trailers for them when I was a kid, and I think I caught them later on HBO later, but I haven't thought of them in ages.  I saw quite a few animated movies on cable TV usually at 5 in the morning because they were so obscure.  Do you remember Gay Purr-ee or Mad Monster Party?  That isn't to say that more recent movies also quickly fade from our consciousness.  When was the last time anyone thought of  Bébé's Kids, Rock and Rule, or Osmosis Jones?   
 
One of my all time favorite movies that doesn't get mentioned a lot is the Thief and the Cobbler starring Matthew Broderick and Vincent Price...at least in the version I saw.  The film has an unusual past since it was released several time in English and each time with some different voice actors taking the roles.  Sean Connery played Broderick's role in one version and an actor named Steve Lively in another.  Wikipedia  I think I might try and find the Miramax version and get the newer release for my collection.  I doubt I could easily find the 3rd version since it was released primarily overseas.

I have to admit I was sobbing like a bitch by the end of GRAVE OF THE FIREFLIES.
 
It's a stunning piece of work and I'm glad I saw it, but I get upset just thinking about it. Especially since I know it was based on the director's real life.

    
 All the Votoms movies pretty much. It's like Gundam, but without all the godawful melodrama/romance that bogs most of that series down. 
 
 

My favorite underrated Disney film is The Emperor's New Groove.

@PenguinDust said:

One of my all time favorite movies that doesn't get mentioned a lot is the Thief and the Cobbler starring Matthew Broderick and Vincent Price...at least in the version I saw.  The film has an unusual past since it was released several time in English and each time with some different voice actors taking the roles.  Sean Connery played Broderick's role in one version and an actor named Steve Lively in another.  Wikipedia  I think I might try and find the Miramax version and get the newer release for my collection.  I doubt I could easily find the 3rd version since it was released primarily overseas.

"

Hell yes! The Thief and the Cobbler! I thought noone knew about it, it's one of my favourite animated films ever. Disney Shmisney.

A Town Called Panic. I talk about this movie on the site approximately  every five hours, but still. It's available on Netflix instant streaming and is worth watching, even if you hate animated films. It defies convention, reason, and logic and is probably the funniest thing I've seen in a long time.

The iron giant is (at least here in Germany) an overlooked masterpiece!
And I love the danish movie Valhalla (1986, I am not sure whether it was released in the US).

@PenguinDust:  Thank you so much for naming that first movie in your post, I've been trying to figure out the name of that movie for ages.

@Pacman said:

" My favorite underrated Disney film is The Emperor's New Groove. "

Hell yeah that movie's hilarious

I always loved Pete's Dragon