While being on a gameplay-mod rage the last weeks, I have to mention one special thing from the modder Deadalus: Complex Doom. In my eyes it honors its name in all regards when it comes to its features:

• Each monster has typically 3/4 tiers where a random tougher monster will spawn in its place.
• Armor and Spheres have a random chance to spawn a stronger type / powerup.
• Weapons have been redone and feature reloading.
• There is an inventory system to make use of items / powerups which are randomly dropped by monsters.
• You can toss grenades and mines with weapons equipped.
• here's plenty more in it but again, its been out for so long people likely know whats what.

Next to that, a lot of additional features have been added since the initial release like upgradable weapons, kicking, demon runes and many more things. For a detailed explanation and a gameplay video, simply check the development and release thread over at ZDoom.org