Justice League (2001)
I have talked about this show many, many times on this blog, and if you haven't watched it already, please do so. While the show isn't entirely Superman, he certainly is featured regularly. Typically, the show follows a few characters fighting off some super-villains, but occasionally there is a big enough threat to require them all. This show has most the classic Superman villains, and while Superman typically has help from the rest of the Justice League, he does do work on his own from time to time! Both seasons are currently available on Netflix!
Justice League Unlimited (2004)
This show is a continuation of Justice League, but includes a huge roster of characters. With this huge amount of characters, Superman kind of has less screen time, but still plenty. Notable villains include Lex Luthor, Brainiac, and even Doomsday in the second season! Both seasons on Netlix now!
All-Star Superman (2011)
All-Star Superman is based on the comic book of the same name. I've never actually seen this, and I might need to watch it soon. The book is very much critically acclaimed, so I'm sure this isn't bad. The movie is more or less about Superman's last days. He gets some kind of radiation from flying to close to the sun and has a few weeks to live. He kind of have a dilemma, does he do everything he has ever wanted to before he dies, or just focus on saving the world like usual. The movie itself got kind of mixed reviews, but it isn't going to cost you anything but an hour and fourteen minutes of your time.
Superman VS the Elite (2012)
This DC animated movie is based on the story"What's so Funny About Truth, Justice, and the American Way?". Superman goes against of new team of superheroes/vigilantes. They are very violent, cruel "heroes". Superman kind of has a big showdown with them to prove some points. The movie has some morals to it, like violence isn't the answer and all that. It's not bad, not my favorite DC Animated film by any means, but worth a viewing.
Superman/Batman: Apocalypse (2010)
As more of a Batman fan than Superman, I am definitely going to recommend this. It even has Batman the Animated Series and Arkham Series voice actor Kevin Conroy as Batman! It is really a sequel to Superman/Batman: Public Enemies, but that isn't on Netflix currently. Regardless, this is still a good movie. Despite the name of the movie, and the DVD cover, and the trailer...this film is really about Supergirl. If you watch it expecting mainly Batman and Superman, you might be a little disappointed. In fact, I fell asleep the first time I tried to watch this, but don't think it is bad because of that.
Superman/Shazam: The Return of Black Adam (2010)
Technically, Superman/Shazam: The Return of Black Adam is a 25 minute short film. DC Animated does these little short films that act as special features on DVDs. These are usually about characters who probably couldn't pull their own movie. They just aren't popular enough apparently. Anyway, on Netflix they have four shorts strung together as one movie listed as Superman/Shazam: The Return of Black Adam. I actually haven't watch any of them yet, and I know very little about Shazam or Black Adam. I know they are arch-enemies, and Shazam is just a guy (or kid I guess), that was chosen to wield this awesome power to fight Black Adam. Shazam is also known as Captain Marvel, but don't confuse him with a certain Kree of the same name.
Justice League: Doom (2012)
I saved the best for last. Justice League: Doom is quite loosely based on "Justice League: Tower of Babel". While I prefer the story in the book, this one of pretty damn good too. As a safety pre-caution, Batman has a file that indicates how to take down every member of the Justice League, just in case somebody goes rogue. That premise alone is pretty damn awesome, but get these files in to the hands of a super-villain, and you have a heck of a story. In the film version, Vandal Savage and the Mirror Master get their hands on Batman's files indicating all the physical and emotional weaknesses of each Justice League member. Savage puts together a team of villains to help him take down the Justice League once and for all. I don't want to ruin it, but for example, they dig up Bruce's parents and when he goes to check it out, Bane takes advantage of his emotional well-being and beats him. If you like the movie, I highly recommend reading it, it is really great!
That is pretty much it for Superman available on Netflix. They are some really old Superman cartoons, but I really can't sit through them. Maybe modern cartoons have destroyed my attention span. Either way, they might be worth checking out! Let me know if I forgot anything!