Project Zomboid. Despite the top down camera and simpler graphics, storms and blizzards have great atmosphere. They make you wanna shut yourself indoors even more than the apocalypse itself.
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Mad Max has some intense and deadly but also rewarding sandstorms
May not be exactly what you're looking for, but subnautica and subnautica below zero are two of my favorite games.
Subnautica starts with you Crashing in a life pod onto an undiscovered water planet and trying to rescue other survivors, gathering resources, building bases submarines etc. Weather is not really a consideration since you're underwater, but there are lots of other pitfalls.
Subnautica below zero is a sequel but set on the Arctic pole of the planet and requires you to go above surface a lot where the freezing temperatures start killing you once you're up there for very long.
The Lazarus facilities in Star Citizen have a constant irradiated electromagnetic storm around them. If you fly too deep (past the facility), your ship will be disabled and you'll crash. You can take a tram deeper into the storm and you'll start to receive radiation damage. So you'll either want a special protective suit, or take refuge inside of facility buildings every now and then.
https://www.youtube.com/watch?v=_OzfPaUWYpY
On this particular planet, your ship can also get hit by stray bolts of lightning (a rare occurence) while flying around any storm . It will shut your ship down for a short time.
On some parts of planets, the weather is cold enough to freeze you (if you're not wearing the right protection).
Some planets are very hot and will kill you if you stay too long outside without protection.
There's an underground prison on a hot moon that you can escape from. If you don't get to a vehicle in time, you'll die from the heat (or lack of oxygen).
I imagine that when base building comes, this'll be an important thing to consider. For the moment, the only two times it has come up as a significant obstacle to overcome in my playtime was during a Lazarus worm thing I did with my org where it took much longer than normal because some players just kept coming back, making the whole thing take twice as long. The second was the Hathor laser which made it a pain in the ass sitting outside the crater with a railgun. Had to take a Nursa to cool down every now and then.
Stalker 2 has very violent thunder storms. The lightning strikes are especially intense.
"There's an Emission incoming. Find cover, Stalker!"
Modded STALKER Anomaly is worth a shout too. Some of the weather mods and sound mods make blowouts extremely intense and impressive.
Flight simulators put a lot of effort into the weather. So flightgear for a free one. Microsoft Flight Simulator if you wanna pirate or pay
Pacific drive?
Just reminded me I gotta finish that one
Still Wakes the Deep puts you on an oil rig amid the ocean in a storm. You spend most of your time indoors though, but there are sections where you get to see the roaring ocean
Well with the playthrough. It's a narrative game, which isn't for everyone.
I loved it.
Stormworks. Obviously. The entire game is about engineering and designing vehicles to go on various rescue missions, or to go to space, or sometimes to mine oil... okay the devs have gone a bit off track from the original vision but the storms are still good for a voxel physics sandbox game.
Looks good, I'm usually not a fan of voxel games but I do see the aesthetic hitting hard in some screenshots
Minecraft
In a similar vein, Vintage Story too.
Rainstorms can last actual in-game days, there are lightning strikes (and a world setting for lightning starting fires), dark clouds, the whole deal.
It's very atmospheric.
I have messed with vintage story for a while, I got into a situation where I was dealing with a wolf stalking my farm for a good month till I finally killed him
No Man's Sky on extreme hazard planets.
Edit: ah fuck, you already said that in your OP, should've read it before 😄
Alan Wake. I don't think the weather is dangerous in of itself, but it makes for a very tense atmosphere.
The Legend of Zelda: Tears of the Kingdom
I was about to suggest Breath of the Wild. The stormy rain is amazing, happens more often and harder than in Tears I think. The constant change of equipment can be a little bit annoying, that's probably why they dialed it a bit back.
The rain with the dramatic music at the beginning of Link to the Past is pretty awesome too.
Heavy Rain is worth playing... For the rain..
Edit: just remembered, there is also that Blizzard-Survival mode in the first Tom Clancy's Division game.
Icarus. That game is amazing. It has varying tiers of storms which damage you but can also knock over trees that can fall on your base (or you), lightning starting forest fires, dust storms making it impossible to see where youre going etc. All the while needing supplies to survive.
Wishlisted for sure
Metal gear solid V
@ me if you get anything good. My recommendation is rain world which is great if you like platformers. The game makes you feel like a small animal in very hazardous conditions that you must often run and hide to escape from.
Ooh I forgot about rain world, that is a very good one, nearly shit myself when one of those chameleons caught me
Frostpunk has definitely storms and hazardous weather, but it's more of a strategy game.
The Last Caretaker is an early access game where you pilot a boat that is often caught is rough storms. Worth checking out.
Dragon Age Inquisition, Storm Coat. I remember that looking real good
Motor storm apocalypse