Game: Torchlight II
Link: Synergies Mod
This adds a new act to the game, over a hundred monsters, new rare bosses, a new class—the Necromancer—more and tougher monsters and the gear to take them on. There are also endgame raids to add challenge once the world is saved yet again, and more on the way—including two new classes (Paladin and Warlock). It's the top-ranked Torchlight II mod on Steam Workshop, and easily the most popular. Be aware that it's still in development, and has a few rough edges.
Game: Civilization V
Link: Steam Workshop
While Brave New World has officially given Civ V a big shake up, for many players Nights remains its most popular add-on. It's a comprehensive upgrade, adding new buildings, wonders, technologies and units, with a heavy focus on policies and making the AI better. The single biggest change is how it calculates happiness, citizens adding cheer simply by existing, but the slow march of war and other miseries detracting from the good times. Annexed a city? Don't expect too many ticker-tape parades. Yet keeping happiness up is crucial, as it's also the core of a strong military. This rebalancing completely changes how you play, while the other additions offer plenty of scope for new tactics and even more carefully designed civilisations.
Ultimate Difficulty Mod
Link: TTLG Forums
This makes Dishonored's enemies more attentive, faster and able to hear a pin drop from the other side of the map. When you get into a fight, it quickly becomes an all-out street war. The biggest change is to Dishonored's second most abusable ability: the Lean (Blink of course being #1). Corvo can no longer sit behind scenery, lean out into an enemy's face and be politely ignored. He's now much more likely to be spotted—especially in ghost runs, where his advantages are now limited to the Outsider's gifts rather than the Overseers' continued lack of a local Specsavers.
Game: Deus Ex
New augmentations! Altered AI! Randomised inventories! Also a few time-savers: instead of separate keys and multitools for instance, a special keyring has both, while upgrades are used automatically if necessary. Difficulty also changes the balance considerably, from the standard game to 'Realistic' mode where you only get nine inventory slots, to 'Unrealistic', which makes JC Denton the cyborg killing machine he's meant to be, but at the cost of facing opponents who warrant it. In this mode he gets double-jumping powers, and automatically gobbles health items when he gets badly wounded. Good luck though, I still got nowhere.