My preferences are Acunetix and Burp Suite (free, though pro sounds cool) + Nikto (open source) and W3AF (open source) mostly.

However, a Web App Scanner can only do a part of the job, you should always check vulnerabilities and potential vulnerabilities manually since there are some that a scanner may never find, for example the latest 0day in vBulletin.

The possibility of a web app scanner finding that, is low due to the complexity of the attack including user interaction.

Most of the time I'm using manual methods especially on well known web applications since the web app scanners only finds common minor risks which is good to have included in the report, but it's rarely I see anything really critical.

The power of the scanner is when it comes to iterations, such as looking for files and directories that shouldn't be there, common vulnerabilities that a hacker might not look for, such as TRACE requests enabled (which has a very low attack vector), public log files which can't be used to penetrate the target, and perhaps backup files which can be really useful. (and so forth)

Good luck with your future penetration testing of websites and of course your choice of scanner and pentesting framework.

Here's the study "An analysis of Black-box web security scanners" (pdf)

It presents an evaluation of eleven black-box web vulnerability scanners.

Sounds like a compelling reason for manual testing to me. That's job security folks!