Neutral and Evil are really pretty close, depending on your map makeup.
With Neutral you get
- more trade routes;
- the best research buildings;
- all tiles automatically terraformed when you research improvement techs;
- a morale bonus;
- and a soldiering bonus when invading non neutrals.
With Evil you get
- +100% economy
- +50% military production
- Free invasion tactics
- Best "mid range" weapons
- Free starbase upgrades
- Other evil civs like you more
With evil it takes slightly longer to get the advantages, because most of them come from buildings from "Concepts of Malice", where as Neutral unlocks all of its potential after "Xeno Ethics". Generally speaking, I like evil on larger maps. The economy bonus is always good, but you need a lot of planets to make the free invasion tactics worth pursuing. Free starbase upgrades are pretty worthless given how useless starbases are generally, but a cluster of 16 military starbases can be a good way to pump your military score.
With Neutral I like them on smaller maps. On smaller maps, trade makes up a much large portion of your income, so the extra routes and resultant diplomacy matters more. The invasion and morale bonuses are automatic and take no further thought or management by the player. Mostly on smaller maps its the best research buildings though. With fewer planets, you don't have an endless number of tiles to make up for a researching shortfall. Depending on map settings, you might only have 10-50 tiles total devoted to research on a smaller map, and neutrality learning centers will really help you on these settings in taking the lead in research. The autoterraforming ability really only helps for soil enhancement and habitat improvement, because once you get to terraforming you can just build the orbital terraformer which has the same effect.
Good gets very little compared to all of the bonuses of the other two alignments. They get a diplomacy bonus, but only with other good races. They don't have to pay maintenance costs on their most populous five colonies, but you would have to playing on a really small map for that to make a difference in your income. They can get base defense boosts, but again, this requires researching to "Concepts" and building a building, and their other three defense boosts are one each to each of the three defensive trees, so you need to research through all three to get the full advantage (where as for evil you can stick to just one weapon branch and do OK, and for neutral the new research abilities come off of core branches). Good can get a building where you increase the chances that people surrender to you, but a) even when you build this it feels kind of hit or miss and

you can turn surrenders off making this ability even more useless.
Its hard to point to an ability that good has that makes it worthwhile. MAYBE the extra def boost if your already playing Krynn and you really want 1.5k defense huge hulls. Pretty much, at this point, any game you see with a good alignment means the person decided to play on a higher difficulty level.
And all of this doesn't even take into account the effects of the random "ethical choices" that pop up as events or when colonizing planets. There, evil really does the best hands down.
Hope that helps.