There is something new around: http://www.sideralis.org/baobab/
Old and outdated answer. The library is not supported anymore.
I used the nstrees library "buggzzy" posted (http://www.edutech.ch/contribution/nstrees/index.php) for a project where I had to give the user the possibility to create and edit the organisational chart of his company.
I like the "Modified Preorder Tree Traversal" algorithm very much but it seems to me that the nstree library is slow. In my case I have to iterate recursively down the tree. Maybe it's something else in my script which is slow.
Anyways I'm also still looking for an alternative and I recently checked the PEAR website and found a tree library there too: http://pear.php.net/package/Tree
The PEAR library didn't seem as comprehensive as NSTREE but I assume it could be more performant.
An article which helped me a lot with this question: Storing Hierarchical Data in a Database