nessus is the best vulnerability scanner around. I have tried many including, Webtrends, CA Cybercop, Symantec Netrecon, and several others.

I would say that the only limitation to this point is it's reporting features. Although it will still generate HTML outputs, along with several other types, it is just not quite as robust in that aspect as several of the others. I also think the setup is about as easy as it gets:

Just run --> lynx -source http://install.nessus.org | sh
or
download it first and run --> sh nessus-installer.sh

Thats it!!