Negative Traits

Most of the "negatives" really depend on how you play the game.

Fore example, low reproduction isn't so bad for an organic race, as they just make replicant facilities in every system, but "Bunglers" with it's shipyard penalty, is a generally bad one for everybody except Temporal races. (as they get super shipyards.)

Personal favorites however:

Physical weakness: I rarely find my ships being boarded, and I very rarely engage in ground combat without overwhwelming numbers to begin with, so it's basically free points.

Environmental weakness: Given that this is basically another happiness negative, I just take care to make them happier than normal.

Foolish: When I actually bother to play with Intelligence active, this can hurt. But I typically have twice as many intel points (points, not facilities) as the aliens when I encounter aliens, so it's not as big a hit as you may think.

Cowardly: I'll sometimes take this if I really need the points for another small bonus, but this can be a big hit. I forget what all morale actuallyt affects, so use sparingly. if ever.

That's all I can recall without checking the game, so I may return with more favored negatives.
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LEGEND:

Stock : refers to Space Empires 4 or 5 as purchased, with no additional mods. Considered to "suck".
BM : short for "the Balance Mod" by Captain Kwok.
Un-named Mod, or Un-named's AI Mod : a replacement AI for stock.

Yeah a -morale trait actually decreases your resource production.

-COMBAT morale give you a relatively minor penalty in combat.

My personal favorite is -radioactives.

Unless you're crystal you don't really need much, even then you'll usually have more than enough.

Depends on who I'm playing, and what advantages I have:

-Organics is good unless I'm biological. If I'm playing BM, I'll still take it, and make sure I get Remote Farming Robots soon.

-Radioactives is a little less likely to show up in my disadvantages list, but otherwise the same as Organics.

-Spying is an acceptable hit if I'm playing against Computers. If I'm playing my brother, I usually have every spying bonus I can get (he loves to spy). Otherwise, as LAG noted, its fairly easy to set it up so you're sabotaging every AI enemy, and defending yourself from the same.

-Accuracy can go if I have a lot of Research advancements: If I'm dealing more damage, I'm more willing to lose some to missed shots.

-Physical Weakness can go unless it's I think I'm likely to get crowded in BM: the militia numbers on a homeworld combined with my preference to take worlds rather than destroying them (especially if I can't colonize them) means it can be very costly to be physically weak and crowded.

-I NEVER slow down production speed. However, I play to expand quickly, take a easily held area, then sit back and enjoy the political and military intrigue, even against AIs. And if you want to expand quickly, slow space yards hurt.

-In general, anything that can be covered up with a small amount of technology is good. Just make sure that you get the technology. This includes not only the happiness stuff, but also all of the resource ones IFF you get Remote Mining quickly, or have a high starting resource amount.

Same topic:
http://home.spaceempires.net/modules.php?name=Forums&file=viewtopic&t=4741