Games

I've yet to find a game that properly rolls in a distant storm that eventually grows into an intense one. They tend to come on very quickly and escalate to 10 in about 20 seconds.

Mafia's "A Trip to the Country" mission has to be up there for best thunderstorm. The atmosphere in the Remake was even better.

From an audio perspective, Terraria has great a thunderstorm effect - just something that really stuck as weighty and impactful

For the whole experience, Project Zomboid isn't a slouch either as it has the audio/visuak effects down and feels better with the some of its parts together as individually there are parts that feel weaker but as a whole makes the for an engaging experience if one decides to wonder during a thunderstorm

GTA3

EverQuest

Uru and Mabinogi has surprisingly good audio with theirs.

For atmosphere, I was floored by Kingdom Come: Deliverance's storms. They really did a good job of capturing the deep rumble of an approaching storm out on the plains.

I swear I've come across an indie game that had great thunderstorms, but I can't remember what it was for the life of me.

That said, imo The Sims as a series has had good thunderstorms. Being outside can result in your Sim being hit by lightning, and iirc there are things that'll increase the chance of getting hit, like being wet, being in a pool, holding an umbrella, etc. I'm not sure which game has the best thunderstorms though.

VRchat has some worlds with really good ambience, and typically they include rain and/or thunderstorms to some extent. You don't actually need VR, you can play VRC on a normal monitor.

I've just realized that one of the things that Risk of Rain 2 is missing, is a persistent thunderstorm that gets stronger as the difficulty gets higher, lowering your visibility over time.

Umineko no Naku Koro ni

Red Dead Redemption, the stormy night in SaintDenis, it really impressed me

The opening act of Little Big Adventure 2 gets my vote.