I like the north quadrant mods, before freeport seven, and there are others but I cant remember them because I have been playing north quadrant too much.

It really depends on what you want in the game. I like new ship designs so I go for mods with lots of ships. Some like new comodities, or others want a harder game. I hate to say it but the question is too general. But in the interest of being helpful, for some mod examples, here's a few good ones in my opinion.
Black label 2.2 by Acid

Evolutions 1.30 by Chips

Discovery 4.79 by Igiss

ARGH'S Tool Kit

These aren't the only good mods or even the "best" if there is such a thing, but they add a lot to the game in either quantity or quality or both.

"we wish for one last landing on the globe that gave us birth, to rest our eyes on the fleecey skies, and the cool green hills of earth" - 'Noisy' Rhysling

I prefer Evolutions 1.30. It's essentially what FL was intended to be: it includes multitudes of novel ship components (capacitators, sensors, power supplies and boosters, engine variants, etc.), in conjunction with new ship variants (many corporations now have unique vessels and all houses have some form of VHF, and most existing lines now have powerful SHFs added to them), capitol ships and actual transports may now be purchased (and capital ship encounters and missions have been added), story systems tend to actually contain dockable bases and things to purchase, new factions, systems, and commodities have been added, and most ships have had a general rebalance (all fighters now have woefully low cargo spaces, but often have modified armour, manueverability etc.). Overall, it enhances FL without utterly changing the focus of the game or the backstory.

I like the froniterspace mod adds lots of brand new systems!
Gotta try it.

Nomads are cheeky
Nomads are sad
What makes me happy is ones that are stupid.

Evolutions 1.30.

Unib5,
Most mods add new systems.


-Burn

The current most popular MP mod is Void 2112.
The server has the highest "verified" active players through the global server rankings.
This might not be what your after, but seeing as it hasnt been mentioned yet, its worth a look.
The mod was built for MP use only. It's not the best mod, but it is a popular one.

website, mod and server password is here.