I have been using del.icio.us since I first heard about it (by reading an announcement of its acquirement by Yahoo!) and I have to confess I was taken by the approach. The only thing I didn’t like was the fact that I didn’t have my bookmarks and the service under control.
Thanks to a note by Erik I found out about Scuttle, an open source clone of del.icio.us which everyone can host on his/her own server. (Please note: scuttle.org only offers their public bookmarking service, the software can only be located at their SourceForge page.) Scuttle is written in PHP and requires MySQL as database backend.
Scuttle offers most of the features of del.icio.us and can even import your bookmarks from there. Some minor usability-issues still arise, but I can live with them. Their API is compatible to del.icio.us so most external del.icio.us applications will work with Scuttle, as long as the tools allow you to specify the URL of the service. Additionally, Scuttle provides three levels of visibility for your bookmarks: public bookmarks, shared with your watchlist (= your friends/colleagues), and private bookmarks.
I installed Scuttle at my company and everyone is busy using it and is happy to now having a central place to store their bookmarks. Del.icio.us was no option for us because all bookmarks are public there.
I can strongly recommend using this software to everyone who wants to have a centralized way for storing their bookmarks without giving away all controls over their bookmarks.
NewsForge has published a nice review of the software.