Wow. People need to re-evaluate. Lost Odyssey, Xenoblade, Conker's Bad Fur Day, Enslaved, Valkryia Chronicles, Silent Hill, Jet Set Radio, Blinx, etc. are hardly obscure. Some of those titles cleared over 500k!
My picks for favorite obscure game would be Nier, but that has turned into a bit of a cult hit.
I'll go with Super Robot Taisen OG Saga: Endless Frontier. This was my favorite DS game. Honorable mentions to Virtual-On, Fragile, Folklore, and Knights Contract.