Board Thread:Questions and Answers/@comment-172.5.13.128-20130117152825/@comment-5886115-20130123120409

Equilivent Exchange 3 is a pretty much complete rewrite off Equvilent Exchange 2. Equvilent Exchange 3 is still a work in progress, so there are a lot of unused items with no properties whatsoever. The Philosipher's Stone is one of those items, as the creator wished it's role to be replaced by the Minium Stone. He still seems to want the Philosipher's stone in the mod, however, and implemented it though he doesn't know what it will do yet, therefore is doesn't do anything.

So use the Minuim Stone, because it's the next best thing.