My own faves
OK, as I came into Linux from Unix anyway, I already had a number of fave commands which worked well going over, including find (especially find . -exec which is damn useful for things like large scale permission fixes), grep and such.
One tool I was introduced to, however, was webmin (www.webmin.com) which is a web based front end which I've used on various flavours of Linux including openSUSE and RedHat/Fedora. It cuts a lot of time and effort out of the everyday configuration tasks on a system. Certainly with SuSE, I can combine procedures using Webmin and YaST, but Webmin takes a lot of the need for tools like YaST and its equivalents on other systems out of the equation.
I'm also something of a fan these days of Nagios (www.nagios.org), amonitoring tool which can be used to monitor quite a large range of devices, from switches up to servers, Linux, Unix or Windows. I tend to use Nagios Core and build my system from there.