I probably should have posted some pictures of examples with my first post but it's always a pleasure to go through game screen shots of games I've enjoyed and loved and post results.
Arcanum
http://i.imgur.com/vxbyZ.jpg
Only one word can describe Arcanum. Heaven. Or maybe it's just that feeling when you make a half ogre that ran away with the circus and uses a 5000 lb rock as a throwing weapon. I need to get a troika tattoo some day. My favorite game in the history of man. If I cannot make a lock picking/smooth talking/semi-dude bro in a game then I will likely go crazy, I love fallout for doing this before troika but I know they had the same people.
System Shock 2
http://i.imgur.com/1NhR1.jpg
And while maybe not the best screen shot of it, there are a few different upgrade stations for the various skill sets and I -love- being able to have full control over that. Every acquired cyber module was like an aphrodisiac.
Ragnarok Online
http://i.imgur.com/CYTPs.jpg
Just one classes skill tree. This game always reminded me of Secret of Mana meets Final Fantasy Tactics meets Diablo 2. Every point was fun to add to a stat or skill, just to see it go up, just to permanently engrave my characters progression by my hand, in an online game, in an mmo where I get to play with others. It felt so good...
Ultima Online
http://i.imgur.com/WONFZ.jpg
Not the full skill list just the crafting section, but seeing a skill increase while taking part in that action while playing the game was just so fun. I was completely addicted to mining and I loved when a vein of ore would explode into my pocket. But being a thief/cook/dead body inspector/archer/bard/animal tamer, I'll never forget those days sailing my personal boat with my pet dragon and being bald and hairless, Recdu Recsu vendor buy bank guards Kal Ort Por. It was made by the same person who made the original Star Wars Galaxies, Raph Koster. I loved making a chunky character in SWG good times.
Etrian Odyssey Series
http://i.imgur.com/Jw6OZ.jpg
One example of a class you have in your party of 5 characters you create. Fun little game that reminded me of Ragnarok Online (even though it was a completely different type of game) simply based on the awesome skill and stat customization and the anime body portraits. Maybe it was all the green that reminded me too.
Titan Quest
http://i.imgur.com/hEvwG.jpg
Probably my favorite Diablo 2 alternative. Sure it doesn't have that amazing necro undead army that D2 has but it's still a lot of fun customizing your character especially since you can multiclass. Plus killing enemies to death so hard they go flying off the screen is always fun.
Vampire the Masquerade Bloodlines
http://i.imgur.com/ViC16.jpg
Another amazing game by troika. Just looking at that picture gives me pangs to be able to click on lockpicking and hacking, I click but nothing happens, I am sad. I will be happy again at the thought of climbing through hotel vents and unlocking secret compartments and finding goofy easter eggs in the process while being a vampire when they were the cool kids.
I personally think path of exile had noble intentions but their tree has mostly passive skills hence the name "passive skill tree", there's nothing wrong with it but it's not my cup of tea. I prefer to press a button and get results instead of just getting a teeny tiny boost.
Some other examples that I won't go into detail but will list are...
Morrowind/Elder Scrolls
Diablo 2
Fallout 1 and 2 + series
Divine Divinity
Divinity 2
Final Fantasy Tactics
Tactics Ogre psp
Other examples include
Gothic series
Star Wars Galaxies *pours a mtn dew on the curb side for the disturbance in the force*
Shining Soul 2
The Witcher series
NWN
Deus Ex
Kotor
Maple Story
Mabinogi
Torchlight series
FF12
And to a lesser extent, Guardian Heroes, SMT games, Castle Crashers, Bioshock series. Maybe Infinity Engine games as well. mm I'm sure I'm forgetting plenty but I wish I knew more, you can tell I live for these types of games. I mostly try to list the ones I had fun with and consider to be quality or at least decent. Ah man it's raining again...