These are a few I've played over the years and really enjoyed. I think most are still available, but some are unfortunately only distributed via discord servers.

No particular order to these:

• Pokemon Prism - A very in-depth mod of Pokemon Crystal with 2 entirely new regions and a large catalog of Pokemon from multiple generations to capture. To my knowledge, it is a successor to Pokemon Brown
• Pokemon Brown - A very in-depth mod of Pokemon Red. This was made 2 decades ago, and was the first mod I ever played. Includes a new region and many Pokemon from different generations.
• Polished Crystal - A faithful (or not) upgrade to Pokemon Crystal.
• Pokemon Crystal Clear - A mod of Pokemon Crystal that brings in many new features and vastly upgrades the AI.
• Pokemon RedStar/BlueStar - A mod of Pokemon Red/Blue that includes the SpaceWorld 1997 assets.
• Pokemon Crystal Kaizo - A mod of Pokemon Crystal that adds in much better AI and a fair bit more difficulty. All Gen 2 Pokemon can be captured and just about every trainer presents a new level of difficulty.
• Altered Emerald - A massive mod of Pokemon Emerald that adds "(almost) every move and ability from gen 1 to 7" along with a few extras while making all 386 Gen 3 Pokemon capturable.

Edit: Just realized this wasn't strictly Pokemon mods... Oops lol.