NYI manages the hardware, I manage the software. I don't have to worry about different system configurations or lacking system software. Performance - A good database design and fast software are the first steps to a fast server. Too many web sites have bad design and try to compensate with fancy hardware. The basis of this configuration is Slackware Linux and Apache web server, but that's just the foundation.
Good design is the most important part.
Security - Security is not black and white. There are different levels for different tasks, and there are many complicated issues involved, but control over the system software is an important step. Frequently, new security holes are found in system software. Linux and Apache are always the first to plug new holes in the shortest time. Keeping up to date on the latest stable software is an area that is too-frequently neglected.