A paper I wrote about HubMed has finally been published in this year's Web Server issue of Nucleic Acids Research that came out this week. It's 6 months out of date already, and the journal has an odd style of putting all URL references inline which makes readability suffer, but it's really just there for people to cite if they reference HubMed (though to be honest it's just as good—if not better—to get a URL reference than an academic citation, especially since I'm not applying for grants any more).
By the way, one reason there are so many papers in this issue is because it's online-only and the journal gets $950 (as an open access fee) for every paper they accept. And there are a lot of web services for bioinformatics, obviously.
The Nodalpoint wiki has a listing of all web services in the issue, with space for user evaluations of each service. Useful criteria would be things like whether the service actually works, quality of the results, ease of use, presentation of the site and availability of source code.