Personally I recommend Zenith Remnant. Golems are awesome, the Dyson Sphere is fun to toy with, several map types, area mines, over a dozen bonus ships, a dozen+ AI types, Cloaker Starships, half a dozen capturables including the Grav Drill and the Planetary Y Boosters.
Second to that would probably be Vengeance of the Machine. Dual AI types, subcommanders, the Wheel map type (my personal favorite, second only to Concentric from Ancient Shadows), Core Turret Controllers, as well as several bonus ship types which are awesome. Protector Starship, Lightning Torpedo Frigates, and the Zenith Hydra.
A handful few things have drifted "into base" from the various expansions (e.g. Neinzul Cockroaches are base even though CoN is the game that introduced the Neinzul faction) but I am not sure which of the things I just listed are in that list. Cloaker starships and area mines, maybe?
Ancient Shadows isn't a bad choice either. Tons of music tracks, two great map types (the aforementioned concentric as well as Clusters) though a little light on other content (I don't use the Champions, which is like the core thing of that expansion).
That said, the "bundle of everything" is like $5 right now on Steam (hooray winter sale). And that's through Jan 2, so its not even a Daily or Flash sale.
