i mod my games up and starsector is no exception. my long mod list:
Arsenal Expansion (does what it says, new weapons/ships)
Combat Chatter (for a little personality to your officers and ships)
Console Commands (honestly for fixing some stuff and minor cheats, like adding a stable location)
Dassault-Mikoyan Engineering (a faction, i like the look of their ships)
Diable Avionics (same as above, a faction)
Disassemble Reassemble (adds some ships)
High Tech Armada (adds some ships/weapons and i think a faction)
Junk Pirates (a faction)
Kadur Remnant (used to be part of a mod i'll list, but its a faction now)
LazyLib (a required library for some mods)
Luddic Enhancement (to give the ludd church and path some extra oomph)
MagicLib (another mod library)
Nexerelin (adds a ton of faction related features for endgame content, including the birth of some minor factions and some destroyed factions attempting to reestablish themselves)
Oga Portrait Pack (what it says it does, a portrait pack)
Outer Rim Alliance (a faction with broadsiding ships)
Ship/Weapon Pack (ships/weapons)
Skilled Up (makes it so its easier to reach high levels)
Stop Gap Measures (some ships and weapons)
Tahlan Shipworks (faction)
Underworld (ships/weapons and a super outlaw faction that will lay on the hurt early game)
Unknown Skies (for some planet variety)
Vayra's Sector and Ship pack (actually 3 mods, these two and that Kadur mod. i honestly cant remember what vayras sector does)
Version Checker (checks to make sure some mods are up to date)
GraphicsLib (ditto like the other libs)