Here's a list of the most popular mods and programs listed together in one topic. If there's anything missing you feel should be added, please leave a note in this topic.
A bugfix patch was created to adress many of the bugs left in the game
Bugfix patch 1.17a - a community patch that fixes bugs, made by the TQIT community across the globe.
Provides completely new locations
Lilith The Will of the Demon: Battles of Jalavia - mostal's huge mod boasts in the entirely new world, Jalavia.
Lilith The Will of the Demon: Battles of Jalavia Masteries Edition - combination of mostal's world with pinkfrog's masteries
Frozen World demo - development has long since stopped. Made by TheBigBoss
Replace the original masteries
Masteries - the first masteries mod, by Pinkfrog
Underlord - fully reshaped masteries, new items, and some added locations and monsters
Paths - by shadowlance
Destinies - by Draeziel
Clash of the Gods - by --Heavy-Metal-Fan--
ASYLUM's Mod - by ASYLUM101
There are several great utilities out to help you with the game
TQ Defiler - allows easy acces to several popular mods at once, as well as editing your character data. Made by SoulSeekkor.
TQ Vault 2.3.0.x - third party program which allows for easy storage (and database extraction)
Miscellaneous - slightly increases in-game storage
The game is generally thought to be unbalanced in the players' advantage. To adress this issue, several difficulty increasing mods were released;
Ubermod - the hardest difficulty mod and also sports new items. Made by Munderbunny.
xMAX - increases the monsters by an x amount. The increased experience grants much faster levelling.
2x difficulty mod - Increases the difficulty by making monsters a lot tougher, adding monster heroes and giving monsters random resistances. Made by luedtke6788
Achilles difficulty mod
Besides the skin section, there are other ways to enhance visual experience
Manastream Animation Mod - It replaces the original animations of your toon
AllSkins mod - gives replacements for your skin.
Camera Mod - allows for nonstandard views
Death Effects Mod for 1.1 through 1.16 and for 1.17 - Replaces the PG-13 death effects with gory effects. Originally made by i.n.s.a.n.e., D.E.M. was updated for fanpatch 1.17 by tatar.spirit
JMD's UI mod - several replacements for the user interface