Edit: The 4 games I posted are only for some examples , you don't have to pick from these 4 games or even these 4 iterations. Post whatever you want.
A lot of RPG/MMO/whatever games these days have their own "Skill Tree".
Just as an example, WoW started off with a 'traditional' skill tree, at the time, very similar to what Blizzard rolled with in Diablo 2. They decided that skill trees with incremental +1% bonuses and such "weren't interesting choices" and eventually went with the talent trees we have now. Essentially (if you haven't played WoW in a while), it's just a few tiers of a choice between 3 talents (screenshot below).
Interestingly Path of Exile decided to turn that whole philosophy on it's head and create a MASSIVE skill tree. Literally epic in scale.
I personally like something a little more balanced like what we have seen in D3. Skill selection from a small pool of abilities and then can enhance each one with a rune. I'm also a huge fan of Rift's soul system. Basically WoW's old talent trees, but you get to pick from a pool of several souls and set up 3 spec trees, and as you spend points, other stuff opens below as you go deeper into the tree.
What has been the best iteration of the "Skill Tree" you have seen?
WoW's Talent System:
Path of Exile's Skill Tree:
Rift's Soul Tree:
D3's Skills Thing: