Ghost in the Shell is hugely overrated in terms of internet presence. Serial Experiments Lain was aired on TV (TechTV's Anime Unleashed R.I.P.) so it has a pretty widespread following. A friend says it's her favorite anime of all time...
That's my definition of underrated too Torillian. And Baki the Grappler is a great example of an underrated one (have you heard of it?).
Iriya no Sora, UFO no Natsu is a good example of an underrated OVA but OVAs are a bit too easy to do. Gatekeepers might qualify but it was somewhat big at one point (not so much now though). The problem is that a lot of popular anime in Japan weren't very popular outside of it. Magic Knight Rayearth is a good example that got a full series and its own line of games.







