Sorry if this has already been answered. I used the search function but couldn't find anything, likely due to user error.

I was wondering what you guys think the most genuinely difficult / challenging NWN mod is. Preferably something that doesn't skimp on the story / atmosphere either.

Difficulty is a funny question. You can always up or down the difficulty slider for combat.

You may have a challenge with story elements (like puzzles) or you may have a challenge of fighting vastly different creatures with different vulnerabilities with limited supplies.

I haven't played any especially hard modules. Just normal figure-it-out puzzles and good combat.

As far as encounters go, most modules use the pre-programmed encounters feature. It takes into account your hero and their party and then builds the encounter based on a predetermined difficulty. So if you have a level 1 and you face an easy encounter, it'll pop a CR 1/4 creature in there. If it's a medium, a CR 1. If it's hard, maybe a CR 2 or 3. The mod builder puts what creatures go where.

I did host a module with some dragons running around and low-level heroes were competing to kill the first dragon. It took a few weeks, but someone was able to amass enough money and materials to build a gauntlet of traps that took a whole dragon down. That was probably rather difficult.

Anyway, that's my input. :D