I am disappointed that this thread is so unpopular. I was considering a reinstall and hoping to find a bunch of cool mods to try.
Me too, I'll add in a few. From what I've used in general, the biggest addons are made by HousePet. They're pretty well thought out, updated regularly, and best of all you can turn certain aspects off if you don't like them (if you're looking for options, they're in game options under Gameplay but I've found they only show up during a game). Best ones include:
-Arcanum, which adds a whole bunch of interesting magic related things. Three new mage classes, some new common weapons (Ritual Blades which are knives that work off of Dexterity and Magic, and Wardstones which are basically a kind of damage reducing offhand weapon for those who don't really want to use shields), new runes, new trees for Alchemist and Archmage, Alchemists can start the alchemy quests from the start themselves, and a school of magic that can teach any non-antimagic character certain spell trees both old and new. One of these trees is rewarded for completing Storming the City by the magic route, making things a little more even on this quest.
-Midnight is an addon featuring Celestials, though not as bit as Arcanum. It adds two new classes, two races, Chants/Hymns get a rework, a whole bunch of new celestial trees, a new starting area for those who'd rather an easier way to begin, and it throws in scepters to common drops for good measure, which are weapons that calculate damage from Constitution and Magic (these may or may not be useful, I turned them off). Weirdly, there's also a couple other minor addons that require Midnight for one reason or another.
-Verdant features Wilders, and is about as big as Midnight but arguably features many more changes to non-Wilder gameplay than it. More infusion options, two new classes in Wilders, a new Rogue class, a slight Summoner rework, and some new trees for Wyrmic as well as a better first talent for Fire Drake (some are unlocked at start, some that unlock upon certain events). This addon works really well in tandem with Arcanum really: Druids can benefit from Arcanum, the Druid's Herbalism tree is both in Arcanum's Alchemist and in the academy, and the combination of the two's new runes, infusions, and egos balance the two.
As for minor things, I've found these nicely done outside of what I mentioned in the OP:
Hexkin Race (it's a fox, entertaining generics aside it plays pretty interestingly)
Blighted Class (Afflicted class that has some Psionic abilities, and focuses on Mind and Blight damage.)
-Wraith Race (A ghostly undead race)
-Vampire race (Undead race that learns Necromancy as it's racials hit level 5. Also comes with a Sunwalker version that revolves around positive energy trees, but Midnight is required for it.)
-Commando class (Basically, it's Rambo. Revolves around unnarmed fighting, stealth, and one-handed weapons. Notable for coming with a bandanna that was actually already in the game.)
-Necromancy+ (A HousePet addon mostly revolving around Necromancer a better class. Also adds in a Spiritmancer summoner/mage class and gives Shadowblade and Doomed a tree or two.)
-Eternal Darkness (Another Necromancer tweak. Adds in a vampirism tree, some locked trees, and regulates Lichform to generics. They're both different takes on the idea, but I like ED a little better. This one's the only one of the two that will work with Deathknight.)
-Spellsword class (This addon started out as an Arcane Blade tweak, and it ended up a whole new class of Mage/Warrior. Each tree revolves around a certain stance and weapon setup, but it's done in a way that you can find synergy with the right items. Pretty fun mechanics as you'll want to have more than one tree.)
-Prowler class (a Rogue/Wilder hybrid that can use either Mindstars or Daggers proficiently. If you're using Verdant you may or may not be interested in this one because of Werebeast and Woodsman already offering takes on this.)
-Pepper Pack (adds a bunnymorph race, some new weapons, the new damage type of Sound, the Bard class which plays as a jack of all trades, and adds a Sound/Light magic tree to Shadowblade. Not bad and Rapiers are useful, but Harps and Singing Swords have quite the limited use for common drops.)
-Nullpack (Adds a huge amount of classes focused on being hybrids. There's some interesting ideas and additions to metaclasses that aren't dealt with by addons very often like Psionic. It tends to conflict with the bigger addons however.)