mathsmum's daughter here
Well, John hasn't written all that many books, which makes it easy cause you can just...you know, read them all
Alaska is certainly his best loved book, but I personally prefer Katherines, and yeah, Paper Towns is my favourite book ever.
He generally follows a similar format, in this fairly ordinary guy (with the possible exception of Colin in Katherines, but even he isn't incredibly complex), this captivating, incredible girl (again, the furthest from this is Lindsey in Katherines, but even she isn't too far from that format) and at least one best friend/comedy sidekick.
But despite the ever so cliche teen format, John just makes it work. Amazingly and beautifully and complexly and wonderfully.
Paper Towns is just astonishing, Katherines is wonderful and Alaska breaks my heart every time I read it.
I cannot recommend all three highly enough.
As for his other books; Will Grayson, Will Grayson...I certainly enjoyed it, but I felt under whelmed by it after his other three. David Levithan and John are both very good authors, but I felt a lot of character development, especially of John's Will Grayson and his love interest, was lost because of the two intertwining plots format just not leaving time for real character development. I also thought that David Levithan explorations of mental illness, though good, could have gone further. The views of homosexuality in that book are brilliant though!
There's still a lot of the same John Green spark, but it just couldn't match his other books the end esspecially was a bit random.
I would certainly still recommend it, but bare in mind that it's not nearly as good as his others.
Let It Snow, his other collaboration books with Maureen Johnson and Lauren Myracle is a lot of fun...doesn't have the same impact of Alaska, Katherines and Paper Towns but it's clever and sweet and really nice to just read and relax and feel good about life.
The only other published work of his I've read is a short story he wrote in an anthology called Geektastic; the whole thing was pretty much a private joke with anyone who watched fiveawesomegirls on youtube (do you watch them? If not I would highly recommend their channel). I really enjoyed the whole anthology, but if you're only interested in John's stuff it's probably not worth the money.
And that's pretty much all he's published...except possibly another short story I think he or Hank mentioned once.