I'm 4000 hours deep into factorio, been playing since I think v0.13? Whenever it first hit steam in 2015.
QoL mods:
- Long Reach: Highly recommended if playing on >1080p res display
- Squeak through: Once you start laying pipes for fluids this becomes an essential mod for moving about your base
- Even Distribution: Evenly distributes items when you click drag to fill multiple entites with items, eg furnaces with fuel
- EvoGUI: Simple display overview for keeping track of biter evolution and basic environment info.
- Vehicle Snap: Makes it easier to align to a given cardinal direction
- Blueprint Extensions mod (Continued): Get the Continued flavor for version >1.0 compatibility. This mod gives some basic tools such as mirroring or rotating blueprints, very useful.
- Bottleneck: shows a simple colored dot over some entities to show if it's input starved, output limited (overfull), or running normally. Makes it easy to see at a glance what is backing up in sections of your base.
- FNEI: Want to know how to make something, or what use a certain item has? this simple mod shows how anything inthe game is made, or everything it can be used in. Also has great mod support, even full conversion mods.
Conversion/Gameplay Changing mods:
- Bobs And Angels modsets: Think you've figured out factorio? Want more factorio? More logistics? More recipes and items to make More things? Step into Bobs w/ Angels modset to ratchet up the complexity by an order of magnitude or two (in a good way). Want an extra challenge? Get the Sandblock mod, which is Bobs + Angels but starting on a tiny island, and you have to harvest resources to build your factory - including the land you build it on - from the sea.
- Krastorio: I actually haven't gotten around to this, but it's another full conversion mod that is highly recommended by many members of the community. Definitely on my to-play list
- Rampant Arsenal + Pitch Black: Want more of a RTS-esque combat challenge? Biters too boring/easy now that you've come to grips with Factorio's core mechanics? Deathworld too easy? Give this ago. It greatly expands the arsenal available to you should you choose to build them, but also greatly ramps up biter aggression, difficulty, and variety, especially at night.
There are many many more mods to choose from, and the modding community is very vibrant, and well supported from the devs themselves, with an excellent mod portal and mod loading system integrated into the game. It's by far the best mod community and integration in a game I've ever seen, and people are still churning out all manner of new and interesting stuff, as well as improving upon the classics listed above. There are also many I've not specified (eg FARL, LTN, etc) that many would consider essential, but this is already a long list.
EDIT: Also just realized this is a 9 day old thread. Came back from the holidays to my desktop and this tab was still open, apologies for the necro.