Just wondering what people thing the best mods are.

(Posting this topic in General Discussion because I am deliberately posing the question outside of the context of a specific game or series.)

Edit: When posting about specific mods, it would be nice if you could mention what game the mod is for.

That "Ghost Master" mod (allghosts) that allows you to replay earlier missions with the ghosts you've unlocked later.

I always like the Francescos mod for Oblivion. It really made it into a much better game. Only partial level scaling, new monsters, higher difficulty, and new equipment.

Gentlemen of the Row

a must have for SR 2.

Based on amount of time played, easily the JA2 1.13 mod for jagged alliance 2, which dramatically extends the game with tons of extra weapons and features. Second place goes to the brutal doom mod. Third place? Possibly the original counter strike mod for half life.
Best mod? If total conversion mods count, then Black Mesa.

A few that come to mind:

Frackin Universe for Starbound.

The Fook mods for Fallout 3 and New Vegas. Plus another million mods I can´t all list here.

Stalker Lost Alpha, a stand-alone mod.

Brutal Doom.

Do total conversions and player made campaigns count, or you mean just smaller modifications to an existing game ?

Also Gentlemen of Steelport for Saint Row 3.

Really? I didn't know about that one.

Far out.

Morrowind Code Patch and Unofficial Morrowind Patch/Morrowind Patch Project
for The Elder Scrolls III: Morrowind. With these added Morrowind becomes more stable and most bugs and glitches that were there are fixed.
Also for Morrowind Better Bodies is recommend, especially if you gonna use clothing mods, such as Clothiers of Vvardenfell. And Wrye Mash. Mash is the swiss knife for handling mods, fix savegames, renumber refs, change load order, etc.

As said Gentlemen of the Row for Saints Row 2. Playing SR2 without GoTR is almost madness. GoTR was made by Idolninja and he added several fixes done by himself and others over at saints row mods and also added optional stuff, such as extra weapons, other gangstyles and the like, all in one big mod. Saints Row 2 is a great game, but was badly ported. GoTR fixes alot, such as the car handling.

The unofficial patch by Wesp5 for Vampire the Masquerade: Bloodlines.

Brutal doom (doom)
Prophesy of pendor (M&B)
Brytenwalda (M&B)
Perisno (M&B)
Synergies (torchlight)
Big world setup and all the wonderful mods it's downloads (baldurs gate - non "enhanced money grab edition)
Osucuros (oblivion)
Open Morrowind (Morrowind)
There are so many it's not possible to list them all, have a look at:
https://www.moddb.com/groups/2017-mod-of-the-year-awards/top100
And for previous years.

For Civilization IV, Rhye's and Fall of Civilization and Fall From Heaven II. Both are one step (or more) above your average mod quality, and really add a lot of value (the former in terms of mechanics and the latter also in lore and immersion) to the vanilla game.

"is a little tricky" - recommended understatement of the year!

Also, Nehrim for Oblivion and Enderal for Skyrim. Really good TC mods that are really original games built in Beth's engines.