I'll back up Eden of the East and Spice and Wolf. I wouldn't say any of the below are hidden per say, but either vaguely unknown or not man people have seen or taken notice of.
Serei no Moribito (Gaurdian of the Sacred Spirit) - I don't see much talk or notice of this series even though I was amazed they aired it on Cartoon Network. I fell in love with it long before and have gone through a marathon of it by myself, with two friends, and even both my parents like it so I've been re-watching it again. The animation is beautiful, the characters three-dimensional, and the setting and circumstances and politics all quite believable even with its fantasy elements. This is one I'll eventually get all my friends to watch.
Mushishi - Another odd one out that people may be starting to hear about but not enough have taken the time to watch. It's a beautiful series, simple pleasing character designs against lush backgrounds with vastly imaginative mushi that effect the world and people and just as many different ways. It's a very calm and soothing anime focusing on a wondering Mushi master in his travels. Each episode stands with its own story from each place he visits, sometimes the stories end happy, sometimes sad, sometimes indifferent but it always leaves a feeling behind.
The Twelve Kingdoms - Sounds like a typical scenario, girl transported to another world but is anything but. The Twelve Kingdoms is full of politics, corruption, people neither good nor bad, youma,talking half-beasts, and an intricate realm that makes the real world seem the odd one. It's such an in depth world and story and there are no characters are stagnant and often go through huge changes. I've noticed a trend, both this series and Moribito were based off of fantasy novel series... so maybe that has carried into the anime enough to really make them stand apart.
Irresponsible Captain Tylor - Well everyone -I- know has seen this series... but that's probably because I've gotten them to watch it (ah the privilege of hosting an anime club... ) Even my dad watched this series twice and I can't even say how many times I've watched it with different people. It's always fun no matter how many times you see it, even the old-school quality about it has its charm.