I'll only put my top 5 because otherwise it gets boring.. I'll also leave out my alliance The Enlightened to keep it neutral.
1. Legends of Epsilon - Since taking in Blades of MAGNITOGORSK (Or whatever it was) they've gone from strength to strength. . . can't argue with their skills, and even though I haven't had dealings with them, they must have a strong leadership team to be able to sustain such a high average, point count and member count. Many other alliances try to do this and simply can't.
2. Pandemic - Although an aggressive alliance I see them as the sneaky assassins. . . mopping up the mess other alliances leave behind and doing it very, VERY efficiently. They are aggressive and although new, work very well together. Wouldn't be surprised if they suddenly came out of their shell soon and really did some damage.
3. The Renaissance - Although I do not exactly take to some of their players, and they can often appear arrogant and rude, I still have a lot of respect for this alliance. They had a big part to play in taking down MM and got what they deserved imo. They pack O44 tightly, it's extremely hard to break in due to sheer numbers of cities. Their only flaw I can see is that without a few key players they would not be as strong as it appears. Overall though an interesting alliance.
4. Nightmares of Elysium - Ok, they've shrunk, and they've been quiet lately which is worrying, but they are one deadly alliance if they want to be. As many others have said, an alliance of 40 active, strong players can beat an alliance of 200 newbie players under rubbish leadership. My alliance has done it in the past with Dineh, but NoE do this on a bigger scale. Much respect for these guys, again quiet lately but hit hard when they need to.
5. Tau Serious - A new alliance. . . not 100% sure on these guys. They seem very organised and aggressive, which is good for their medium size. I'm rating them bottom of my ranks because I don't know enough about them to elaborate, but from what I've heard they are a collection of organised players from various alliances, including Silent Chaos.
Other Alliances
The only other two alliances I have some respect for are Renegades and One For All. Renegades, although don't appear strong, are organised for their size and can easily put off another attacking alliance if they want to.
Even though One For All have my alliance marked as enemies for no reason (lol), I still have some respect for them. To retain an alliance of that size, keep it top of the rankings without taking much damage takes some good leadership. Whether this be good in terms of support and activity, or whether they have a good recruitment technique to replace lost players, somehow they do it.
I don't know enough about any other alliances to comment. I have my opinions, but they are mainly based on rumours.