We're working on that. I DO tell people to check plugins first (note: check, not blame), but also to see if the readme.html page loads super slow or not. It's a give-away that it's probably the apache service. That said, we should have that fixed for most servers now, and the weird slowdown should stop happening.
If html and php are slow, it's probably apache.
If all PHP (including a php info page) is slow, it's PHP (though that may be caused by WP sucking up PHP memory)
If WP is slow, but a phpinfo page is fast, it's WP.
(Not always, but you get the idea)