What do you run on your website? Do you have a LAMP stack? That’s Linux, Apache, MySQL and P{HP,erl,ython} for the uninitiated. I normally run a LAP/LM app stack duo. This allows me to separate the MySQL database from the web stack, and use it for other purposes as well. I include such services as xbmc and MS Access/Libre Office Database as MySQL clients as well. It makes sense to isolate the MySQL server.
There are also several web servers, or LAP stacks in my home. I keep one instance for my production site (this page here), and a handful of others for testing and development. They all share the same LM stack.
Recently I was required to produce a WIMP stack, that’s Windows, IIS, MySQL, and php, for development purposes. The architecture is almost completely different, but it’s now using my LM stack for database as well.
There are a few things to consider when you’re deciding between a single LAMP stack (or multiple LAMP stacks) and a LAP/LM stack.