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Automated web app security tools are helpful to a point and should be a part of your security assessment toolkit, but not the only part. Every web application is different, business logic testing is hard to generically automate, and AJAX just makes things more complicated. From my experience, tools will often miss issues that a somewhat skilled tester can pickup with minimal manual effort.

Be careful with Skipfish, it can generate a significant volume of traffic that'll peg a production server pretty quickly.

Also worth a look:

http://dirb.sourceforge.net/ (you'd be amazed how many high-risk vulns this simple dictionary-based content discovery tool will help find)

http://www.cirt.net/nikto2

http://www.websecurify.com/

http://o2platform.com/

http://www.owasp.org/index.php/Category:OWASP_WebScarab_Proj...

http://portswigger.net/scanner/

http://www.owasp.org/index.php/Category:OWASP_Testing_Projec...

I think Google released something similar a while back ago. Anyone remember the name and link?
There are SkipFish and RatProxy

http://code.google.com/p/skipfish/

http://code.google.com/p/ratproxy/