I'm a PC gamer and I like keyboard and mouse. I don't own a console. I'm open to the idea that some game types might be better with gamepad/controller(after getting used to). I already got HLD bundled in a promotion I don't remember.

What are the best PC games that are genuinely better played with a gamepad rather than keyboard+mouse? I'm trying to justify a gamepad purchase.

This is not always obvious. For example Nuclear Throne appears to be a console-like shooter, but in fact keyboard+mouse has some advantages. High precision weapons like crossbow work better when you can aim quickly from a distance. Or maybe if you play as the Fish character?

You mentioned Nuclear Throne, so I'd like to add that Enter the Gungeon and Atomicrops are similar games which certainly benefit from using a controller instead of kb+m.
I can't speak for NT because I haven't played it, but EtG and AC reward the "focus on your character, not your target" mentality and playing with a controller (with aim assist turned on) makes that a lot easier.

I do feel that Hyper Light Drifter is much more comfortable with a controller.
A lot of platformers, RPGs, racing, and hack-n-slash games are also great with one - Hollow Knight, Crawl, Cuphead, Katana ZERO, Slipstream, Yooka Laylee games, River City games, Falcom titles, Baldr Sky.

Pretty much anything that doesn't rely heavily on precise reticle or camera movement (like FPS, RTS, building/management sims do), a controller is fine - or more comfortable! - to play with. :D