It seems relatively easy (ie. zero configuration) to get PHPstorm and Xdebug up and running together, so I will presume you have that going. It often happens that you want a breakpoint in a frequently called function. Just putting one will make the system stop there every time. After a right click, Edit you can add conditions to it which help. Even better, you can add a breakpoint to somewhere else, remove the suspend checkbox from it and make the first breakpoint disabled until the second is hit. This allowed me for example to break in drupal_flush_all_caches only when fired from WebTestBase::resetAll.
Another useful tip from dawehner (I had no idea!): PHP CLI works with xdebug just fine, you just need to run
export XDEBUG_CONFIG="idekey=PHPSTORM" first.