Well, the Japanese teams don't make many non-FF/DQ/KH games anymore, so the thread title forces us to look to the output of their western colleagues. Their games are distinguishable from titles mentioned here like Star Ocean and Bravely Default, that truly were made by outside studios. At some point we need to accept the Eidos devs are Square Enix employees and if we want to exclude their games from conversations about Square, then we need to do the same for Dragon Quest games, especially the ones developed by Level-5, Heartbeat and Chunsoft (which is all of them).

If you had to twist my arm, I would say Tactics Ogre: Let Us Cling Together, which I only omitted in the first place because some EoFFers get quite upset when you treat it like a new game...