Roland Krause bookmarked a great post: "Why Web 2.0 is failing in Biology" by David Crotty. That I got to know about this post just by subscribing to his links in del.icio.us is a success of Web 2.0. I'm just not sure if the same successes are already in reach in the context of science. I especially agree with David Crotty's observations about entry barriers: Unless new tools/communities make it very easy to use them and provide great benefit, the rate of adoption will be low.
From my personal experience, I can share this: Almost two years ago, I participated in giving a series of talks about Web 2.0 and how it might impact biology. Looking back, I'm not sure many things have changed. I have been using CiteULike for the past three years or so, but I think I will now switch to Papers. CiteULike allows me to bookmark and tag my papers, but when I search my library I mostly use a custom Google search for the specific author.
Papers lets you easily create a collection of all PDFs you ever read. Thanks to Spotlight, you can perform full text searches on the articles and quickly retrieve the paper you have in mind. This avoids the overhead of applying tags to papers that you actually don't end up using. (GMail is another case in point: a quick search function eliminates the need for an intricate folder structure.)
I can't remember a specific case where the "Web 2.0" functions of CiteULike ever worked for me. Peeking in the bibliographies of other people can be interesting if you have some bookmarked papers in common, but the signal-to-noise ratio is very low. So, unless you know specific people or groups to follow, you'll most only use CiteULike in "Web 1.0 mode". And then we come back to the initial observation: If a web tool is more complicated or less featured than the desktop (or even, paper) version, it won't be used much.
Update: Mendeley might be the Windows equivalent some of you have been looking for (15/08/08, more in this post).