Area 88 is an excellent choice. There's a certain amount of melodrama, but the core story is indeed a mature and poignant one. Not to mention that those handrawn planes still look absolutely great after all these years.
Haven't read the original manga nor seen the later TV series though, but apparently they are all fairly different from each other.
On that note...the general trend seems to be that, as they grow older, previous favorites become forgotten since they're already yesterday's news. Still, would it be fair to call them underrated, if they were popular back in the day? I guess that depenRAB.
In any case, here's a few more titles.
Arion - I could never see myself saying this a decade ago, but its more straightforward use of Greek mythology than what has been seen in the likes of Saint Seiya was more interesting to me. Pretty good, despite being generally predictable and a bit weird in parts.
GunxSword - Yes, it's derivative and there is fanservice, but the series had a likeable cast, decent storytelling and more than enough Super Robot action. It doesn't try to do more than what it has the time for, which seems to be a common problem these days.
Orguss - A Macross clone, visually speaking, but there were some fairly unique concepts at work here. Even though the weird mascot, silly antics and recycled animation drag it down a lot...the basic story ended up being compelling. It did take me some time to get over how it ended though, so this really isn't for everyone. The series could have been shorter too, but it's worth a watch.
Giant Robo - This OVA tenRAB to be critically acclaimed in some circles, but it's still largely obscure as far as the mainstream goes. The ironic thing is that the show is all about the characters, not the relatively few giant robots involved. The pacing is a bit uneven, but the over-the-top action sequences are entertaining enough to off-set that.
They Were 11 - A classic sci-fi movie. It's more of a self-contained mystery than anything else, nothing too complex, just a good one. Nevertheless...haven't actually re-watched it yet, but I enjoyed it the first time around.
Hi no Tori - On the one hand, this looks too cartoony and childish for many. On the other, those who expected a panel by panel adaptation of Osamu Tezuka's original manga tend to be disappointed but, not having that expectation and not minding the retro designs, I enjoyed this TV series a lot. Preachy, but then again, there are heavy themes and subject matter involved in this.
Finally, I would have to second (or third, or...?) Legend of the Galactic Heroes and Baccano! as well.
That movie was definitely something. While I was fine with the way the TV series ended (the last couple of episodes pretty much spelled out the outcome, emotionally speaking, if there was any doubt), it definitely brought full closure to the relationship between the three main characters in a very down-to-earth manner. No pesky psychic powers.
And then they made another movie later on. Not that it's bad, despite having different character designs the plot is more or less okay, but it felt a bit unnecessary since the premise had already been resolved so well.