I would say Morrowind had the most worthwhile exploration. You were constantly finding little hidden secrets everywhere. Whether it was a new book to read, or a sword, or a legendary item, you were always finding something. I love the handplaced feel of Morrowind, where you can find a mummy who's holding a glass halberd, or has a book between it's hands. And then exploring houses and where people lived was great too. You never knew when you find some interesting book or potion laying about. Morrowind is the ultimate exploration game.
Divinity 2 has worthwhile exploration as well. It seemed every nook and cranny of the map had something to find if you searched well enough. Could be a wishing well that grants you an experience bonus, or a new quest, or a storage shed with goodies inside. There was always something to find and you were rewarded for scouring every little bit of the map.
I'd also mention Lost Odyssey and Blue Dragon as being cool to explore. NPCs were a big reason to explore, to talk to people you normally would miss if you just rushed through the game. But also finding hidden items in urns, chests, cabinets, etc. There was always a chest to find in some remote location on the map that had something worthwhile in it. Both these games had a lot of stuff you could miss if you weren't thorough with your searching.