I'm going to hazard a guess of Monster Hunter World?

Adding final clues for #40 and #39 which should make guessing them simpler.

40 - Crash Bandicoot 2
- If you go against one of the main conventions of the game in the first level, you’ll be rewarded.
- Your foe is now your friend… or is he?...
- …Your sister certainly doesn’t believe him
- This was her first appearance in the franchise. She would become playable in the following game.
- The first clue refers to the destruction of boxes / crates

39 (incorrect guesses - Castlevania: Rondo of Blood)
- A launch title for the first system it released on, it was sometimes criticised for having dark visuals that made it difficult to play on original hardware (subsequent hardware revisions remedied this issue). This is supposedly the reason the next game had brighter graphics.
- There are four unlockable modes, each of which give your character a boost on one specific attribute at the expense of others - magic, strength, subweapons, and luck.
- In some regions, this game shared the same name as the very first game in this series (other regions added a subtitle). Funnily enough, that first game was later released on the same system, as one of a number of classic games that were reissued.
- The most recent re-release of this game was on multiple platforms, as part of a collection with three other games from the same series.
- Your character carries one of the series’ most iconic weapons as he aims to vanquish a familiar vampiric foe.

37 - Resident Evil Remake
- What once got you access to the garden, now allows you to collect a powerful weapon.
- What was once permanently dead, may now rise again should you not take the necessary steps to prevent this.
- What once prompted a neat little cut scene, now allows an enemy to enter the room.

Current list - https://gamrconnect.vgchartz.com/thread/247804/the-official-thread-the-14th-annual-greatest-games-event-post-only-once/4/#3

40) Crash Bandicoot 2?

39) A Castlevania, but I don't know which. Rondo of Blood?

37) Resident Evil Remake?

40 and 37 are correct. 39 is the right series but wrong game.

Clue wise, the first for Crash 2 references the gem in the first level, which you obtain by completing it without smashing any boxes.

For RE Remake, the first clue refers to the crests now being used to get the Magnum, the second refers to the Crimson Heads, and the third interacting with the front door, which now lets in a Cerberus if you check it.

37. The Wind Waker HD
It might be a bit unfair to specifically list the remaster when the vast majority of the credit goes to the base game, but the small improvements present in HD really do make it the the best version of the game. The graphic upgrade is the obvious, but more important are the various little QoL improvements like increasing sailing speed and cutting out the busy work from the Triforce shard collection quests. The game itself, however, deserves the bulk of the credit. Exploring the ocean, even at the original slower speed, was incredibly fun and I spent a couple hours just filling in the map the moment I was able, perfectly happy to put the main quest on hold. The dungeons and bosses weren't the greatest in the series, but the game made up for that with a fun combat system and how expressive and enjoyable Link was. It felt for the first time like he really had a personality all of his own. And to this day WW Ganondorf remains my favorite iteration. His presence, his speeches, and most of all the final fight as he knows he's lost, but is determined to take you with him.

Apparently these are tricky. Let's give them a third hint that'll hopefully shove some of you the right way.

#40: Probably the coolest special edition I own is the one for this game, it comes with a wooden miniature of an Onager that you could build yourself.
Hint 2: At launch the game was criticised pretty heavily by players however. With a slew of updates adding things like a family tree and overhauled politics, much of this criticism has subsided.
Hint 3: It also features something that was sadly cut again in entries after this game's direct sequel, namely that cities would 'grow' on the map as you upgraded them instead of cities being represented by a sort of 'model'.

#37: Technically just a sprite swap of another strategy game, and considering the franchise this is part of, shouldn't they have done more?
Hint 2: The basis for this game is a famous rts from an otherwise completely unrelated franchise and developer, but my game's gameplay is basically exactly the same, down to the building types and technology (in the sense of advancements and upgrades for the purpose of the gameplay).
Hint 3: For example the original game's 'Barracks' is now a 'Troop Center', the 'Castle' a 'Fortress' and the upgrade 'Heated Shot' is 'Ion Accu-Accelerator'.

#36: A handheld entry in the series which unlike its console brother actually is a numbered sequel.
Hint 2: These two games were released pretty much simultaneously.
Hint 3: And even though other games in the series would release in between, the next 'numbered' sequel wouldn't release until about 19 years later. Guessed by Veknoid_Outcast - Metroid Fusion

I agree with the bit about the remaster. The HD version was a very good remaster, it really improved my opinion of the game.

Yes, you're both correct. 

#37 Concept art of a semi open world platformer where you collect eggs

Maybe 40 is civ 6?