Kingmaker gets my vote wholeheartedly as the top AP.
Edit: Ohhh forgot to explain why:
It fits my style of play. I prefer to have a goal and let the players get their of their own accord. Along the way they have encounters, but it is when the players decide to deal with it or when they stumble across it is when they deal with it.
Compare that to Curse of the Crimson Throne. One of the adventures, our group was told right from the outset, "you have to do X. But to be able to do X you have to first get magic item Y. But to find out exactly how to get to Y, you have to first be trusted by Z clan. To be trusted by Z clan, you have to be have someone from clan A who is highly regarded for their neutrality watch you perform operation B." I didn't find that adventure alot of fun. Why couldn't I just goto clan Z and kick the crap out of them until they told us where Y was. Why couldn't I just use magic to figure out where Y was? Its our adventure, why can't we do it the way we want to do it.
And that's what Kingmaker does. Here's your goal. If you want to skip the rest of the adventure and go straight to the main bad guy, go right ahead. You'll be at a lower level and it will be difficult, but it can be done.
I really like Kingmaker for the reasons listed above, as well as for the kingdom building rules it introduced.
But my favorite so far is Serpent's Skull. The first installment is almost pure sandbox (like Kingmaker), but I love the flavor, and I love the way they've detailed the NPC interactions with the party. Also, the choices the party makes early on regarding the NPCs will have far reaching effects through the story.
I've done Second Darkness, Kingmaker, and am now on Rise of the Runelords. All of them have been fun, but Kingmaker is my favorite so far. I like the perfect balance of story, sandbox, and goals.
I liked all of them to one degree or another. Some of them appeal to different play styles or themes. Which will have a lot to do with which one you like best. So I will list them in order.
These are all very good.
1) Rise of the Runelords
2) Kingmaker
3) Curse of the Crimson Throne
4) Serpent's Skull (this one is not all out yet so it might be moving up the list)
These are good
5) Legacy of Fire
6) Council of Thieves
I have played in Second Darkness, Curse of the Crimson Throne, and am currently playing through Legacy of Fire.
I have GMed Rise of the Runelords, Curse of the Crimson Throne, and am presently running Kingmaker.
I've read through Crown of Thieves and Serpent's Skull, but will exclude them from ranking, as I have not experienced them in play.
1. Rise of the Runelords.
This is honestly a very close race along with Kingmaker. RotRL edges the others out for me because it was an excellent introduction to the adventure paths and Golarion in general, and Varisia specifically. The party gets many memorable encounters, and a truely epic villain. The gold standard for the Paizo adventure paths.
2. Kingmaker
My players are just now getting the kingdom-building stages, but love the sandbox style of adventuring. As a DM, I also enjoy the option for lengthy time-lapses between adventuring sessions, as the meteoric rise to power of the PCs in any adventure path does strain credibility a bit for me.
3. Legacy of Fire
Part of this is a personal fondness for genies and desert adventuring. My group is only just starting adventure 3, but I've really enjoyed how fleshed out the background is. I can't speak for this one from a DM perspective, but I really like all of the flavour. My GM had toyed with adapting some of the Kingmaker kingdom rules for Kelmerene, but ultimately decided against it. Once again, points from me for allowing lengthy breaks between the adventures.
4. Curse of the Crimson Throne
Both as a player and a GM, I enjoyed the continued fleshing-out of Varisia, the story of the Vancaskerkin family, and the story of Korvosa itself. That said, there were a few things that stretched my disbelief as this adventure path went on. Most notably is the
almost overnight appearance of the Grey Maidens as a credible military force within the city, displacing the established city watch and military orders almost completely. The players are also encouraged to tie themselves strongly to Korvosa, but spend almost a third of the adventure path away from it. My understanding is that this was somewhat addressed in Council of Thieves, which is complete city-based.
I also think that a fair amount of the Crimson Throne is _very_ linear (talk to group A to get an item for group B who will give you access to group C, who have the information you need), but Paizo does try to address this in side bars for groups that want to stray from the path, and experience the adventure in other ways. The GM will have the tools, but will need to put a fair amount of effort into using them.
The default path in adventure 4 is probably the most respectful to the Shoanti clans, so I think a good-aligned party or one containing Shoanti characters are the most likely to take it. Impatient, or more neutral/evil aligned parties would likely be less inclined to do so.
All that may sound fairly negative, but I thoroughly enjoyed CotCT as a player, and my own players seemed to have similar fondness.
5. The Second Darkness
The weakest of the adventure paths is still fairly strong. I do feel that there is some discontinuity between the first two adventures in the series and the rest.
A great deal of effort is made to get the players interested in running the Golden Goblin, but it barely shows up after the first adventure. Our group also felt like we were constantly being lead around as cannon fodder or living shields for the elves for the last 4 adventures, with very little consistent pay (a big thing for our primarily neutral, but evil-leaning party). That said, it was nice to have the third of Varisia's four cities fleshed out, as well as a great deal about the elves, and the drow of Golarion. Spending time in Zirnakaynin posing as drow was a great time.
If I run another adventure Path, I am undecided as to whether it will be Council of Thieves or Serpent's Skull. This thread may help me decide.
I don't know all the APs so I voted for RotRL that I played (well only the 1st half but it was really good) and Kingmaker that I'm actually playing.
I read CotCT and I found it not so good : the basic idea is good but I didn't like the way it was treated. The BBEG (big bad evil girl ) is identified at the very beginning and one of the 6 adventures is just a big stupid dungeon crawl.
I don't really know about the others APs : I was interested in the drow one but I heard it is not so good.
I don't know all the APs so I voted for RotRL that I played (well only the 1st half but it was really good) and Kingmaker that I'm actually playing.
I read CotCT and I found it not so good : the basic idea is good but I didn't like the way it was treated. The BBEG (big bad evil girl ) is identified at the very beginning and one of the 6 adventures is just a big stupid dungeon crawl.
I don't really know about the others APs : I was interested in the drow one but I heard it is not so good.
I agree with what one of the previous posters said about second darkness in that early on there's lot of focus on riddle port. then bam no longer of any real focus in the ap. however the AP has ALOT of golarion history in it that I think makes it well worth playing.
) is identified at the very beginning and one of the 6 adventures is just a big stupid dungeon crawl. 
