play it out of the box for the first game, no mods.. it's pretty cool like that. mods are good but often mess with the balance, as they base the npc's (non-player character, AI) encounters on teams of players v's teams of npc's and so a single ship gets ripped up pretty fast.
before installing any mods, make a backup of the files in the root (i.e. files in "D:\Games\Freelancer\") also both data and exe folders (about 520mb zipped up). then if something messes up while removing a mod, just restore these backups. you'll find pretty much everything freelancer at
www.lancersreactor.com, if not you'll find a link to it...
mods to check out at sometime..
Evolutions, Epsilon, HostileUniverse and FlRebalance..
it depends how you want to play though to what mods are usable, some are setup to be played only on their server/s. others are setup to be hosted as multiplayer and do not support singleplayer at all (apart from connecting though the localhost/ip and so playing on your own server). others support singleplayer but with no storyline (like playing online but on your own), a few support storyline but as i say, often there are balance issues or bugs..