Final Fantasy 10's is my favorite for sure. It looks a lot like Path of Exile's, but FF10 uses it for everything involved in levelling up: skills, spells, and stats. Your characters move around it, paying a number of "spheres" for every move. All the characters use the same grid but start in different locations. It makes for a fun sort of mini-game, going through that maze of a skill tree!
Honorable mention to Sword of the Stars'
skill trees (skill forest?). Not only are there a whole bunch of things to pick from, but the trees also change from race to race and from game to game. For instance, some races are good with shields while some aren't. The races that are good with them will have a high chance of being able to research "Shield 1" while the races that aren't as good with them will have a low chance. At the start of the game, hidden dice are rolled to see if the player can research each tech. The races that are good with shields will probably get them and the races that aren't probably won't - but that always won't be the case. Every time you play, even if you stick with one race each time, there will be some techs you won't get that you usually do and some you usually don't see but get to research in this play-through! It makes replays much more interesting.
Another honorable mention to Metal Gear Solid V: Phantom Pain's
equipment upgrade tree. Mostly because I didn't expect anything even remotely that deep to be in a game like MGS5
P!