What are some important MySQL status variables to keep an eye on? I'm a fairly new DBA with a programming background. As such, I like to build tools to manage tasks to help me familiarize myself with the intricacies of a technology. 

In this case, I am managing multiple MySQL servers and would like to build a UI to view the health of the servers.

What are the important status variables to watch out for that throw a red flag that something isn't right on a long-running server (>48 hours)?

An example of what I'm looking for is qcache_lowmem_prunes becoming larger could indicate a misconfigured query_cache
Here's a link to a bunch of links on "tuning best practices."

The short form is: It depends. What are you tuning for? Tuning read performance is different than write performance and everything changes when you move to a cluster. There is no one set of "magic variables" that can be quietly optimized for every situation.

From these, you can look at monitoring variables, as the variables that need to be tuned are strongly related to the variables that require monitoring.