I looked at an SQL server today from a customer, talked with one of their devs and he said that he's unable to understand why the server misbehaves... All (!) queries were optimized, but they have 'big data queries'... Migraine started, I had a very bad feeling. Monitoring? Nooooppeeee. Migraine kicks in. Connected to server. SHOW GLOBAL VARIABLES...
After a bit of scrolling I found a lot of misconfigured variables (e.g. extreme large join buffers, unrealistic buffer sizes), high slow query count (nearly 60 % of COM_SELECT) and a few variables that were unknown to me.

Then came the version line.
5.0.46
Yes. 5.0.46.

Big data? Well... 30 GB of usage data.

I called the company back... The dev told me sternly that this was the production server (I had hope...) and that I lie - neither the version, nor the variables could be the problem.
A coworker had to verify it and our manager had to do the communication... Worst, most traumatic working day I ever had.