This is exactly what SparkLab aims to solve, take a look here: http://sparklix.com/demo-movie It's free for academic and non-profit organizations. Personal free edition will be up later this year.

You may be interested in SparkLab 360: http://www.sparklix.com/product/sparklab . Aside of document management it also provides functionality specific for biological research such as reaction calculators and experimental data analysis, and allows you to associate documents with your lab protocols and experiments. It's very "Web 2.0-ish" and cheap (free for academic use).