I was contacted to take part in an e-consultancy review of Online Project Management a short while ago, and received a link to their report on best practice in this area today. [UPDATE 16/05/07 - Linus Gregoriadis, Head of Research at e-consultancy, let me know I was pointing to a link for survey participants only, so - just in case you have bookmarked this, the link has now switched.]
I have to say, having skim-read the first-half, that it very much matches my experience. For instance, as a PRINCE2 qualified practitioner, I would have to agree that the PRINCE2 "exception"-led model of change management (and over-reliance on detailed specifications) can work against managing rapidly moving Web projects (where XP and other Agile methods build this into a rapid and iterative loop).
The great thing about a Web project is that you can manage the overall project with one methodology and branch off (in a controlled manner) software development, for instance, in a slightly different direction. I think it pays to be cute and take a pick-and-mix approach, rather than try to adhere to a monolithic approach, all in the name of getting things done. I don't think this has to be at the cost of losing control of time, cost, quality and associated risks; this is one of the reasons that I enjoy Basecamp as a Project Management tool: it helps me control the project while being flexible enough to stand setting up PRINCE2-type methods, controls and stages as categories.