I enjoy playing all 3 alignments. I've probably played 5 games as Good, 10 as Evil and 20 as Neutral. If the game is about role play then I think you should stick with the one that suits what you're race is about. However if you are min-maxing for me (based on suicidal/no tech trading/conquest only/random map sizes) there is only one winner.
My observations are:
Evil
On tiny maps there is a tendency for quick conquest, in which case Evil bonuses are better than on large maps.
Evil's bonus are good at spending money. They have weapons that need a lot of mp's but a building that creates mps.
You just need a good economy to support evil's strategy. In general if you are going to win as Evil you probably need to win quick... or at least get into an unassailable position quick. I tend to go for invading homeworlds in the first couple of years if I can. The AI has a tendency to stick most of its development into its homeworld in the early years, so if you capture that you've completely neutered their development. Evil with its bonuses is great at going for that early rush.
Good
I only play conquest with no tech trading and so Good bonuses are nerfed. I can imagine if I was going to an Alliance win I might think very differently. On my settings the Good techs are uber expensive to put to use on ships but as the research also adds to all defence you can generate very high def numbers (especially if you play the Drath). There is another big thread about the whole defence vs attack debate. I personally think it is weaker than the other two alignments. The other bonuses often mentioned is "Good races attack you less". With a conquest strategy this can lead to you being able to focus on getting rid of the Dregnim, Korx and Yor early on then being able to pick off the others at your leisure. The problem I have with this is if I can conquer 3 races I'm generally over the hump in any case. All this is doing is buying me time from the other Goodies. However a strong military and the Spin Control centre has the same effect but for all races. So as I said I find Good the hardest (and sometimes therefore the most enjoyable) to play on my settings.
Neutral
For me the Neutral bonuses are huge.
I don't need to go anywhere near one brach of the tech tree. (Terraforming)
I don't need to lose the time building terraforming squares.
I am almost certain to be ahead in research due to NLC.
If I'm ahead on Tech I can get to the important wonders/trade goods first which in turn puts me further ahead.
I can get on OK with both Good and Evil civs which again buys me time to pick off opponents one by one.
If I'm truly min-maxing I would go for Drath... Choose all the evil planatary options I could (up to going Neutral)... Then choose Xeno Ethics with no cost. This seems to me to be the best race/options/alignment path by some distance.
However it is probably not the most fun to play