Harmony first, then Core and the DLCs, followed by library mods (like Hugslib, JecsTools, Graphics Settings, Humanoid Alien Races, Enable XYZ), miscellaneous/minor mods (2), CE, VE(1), then Race mods (AT belongs here), other big mods(2), [REDACTED (18+)], Character Editor(3) and mods that change other mods (Patchers, patches, tweaks, etc.), Mods that change pawn behaviour (Replace Stuff, Pharmacist, Quality Surgeon, CommonSense), ModManager and lastly performance mods (RuntimeGC, Dubs Performance Analyser, Performance Optimizer, Rocketman OR Rimthreaded.

RimPy and Fluffy's ModManager do the obvious stuff. You still have to do the rest manually! (RimPy has been abandoned. Use RimSort[github.com] instead.)

(1) If a mod disagrees with my list, trust them instead! These are general guidelines, not set-in-stone rules.

(2) Mods that add just normal buildings like you can find them in vanilla count as minor to me, while mods that add new mechanics, like fridges, ceiling-mounted lamps or large amounts of new buildings count as large.

If you're unsure, check the steam page of the mod in question, take a look at the bug reporting page or comment section for any recent tips and go from there.

Ultimately, it won't have much of a significant impact on your gameplay, whether you decide that a mod counts as large or small, and misidentifying one will at worst affect performance in the single-percentage range unless you overlooked something serious that should've been marked as such in the About.xml by the author.

(3) If you use Prepare Carefully, remove it asap! It destructively patches pawn gen and will cause issues! It is also called every time a pawn is generated and as such slows down the game tremendously when generating raiders for example.

If you need a replacement, try Character Editor + RandomPlus! It does everything PC does, better and more! The UI takes some getting used to, but once you've figured it out, you won't want to play without it anymore.