An old but worthwhile [article by Nielsen about multiple searches][1] says: 

> What matters [...] is not the implementation, but the user experience.

Regarding your observation about different datasources: if that is the case, it would be relatively easy to combine a single search box with a datasource selector (e.g., one search box but a selector with options like []Search Users []Search documents []Search Projects). 


  [1]: http://www.useit.com/alertbox/20030224.html