We're currently in the process of migrating web server to a new Ubuntu 14.04 box, and we are running into the same problem across our multiple Craft installations which is majorly affecting our workflow across all projects at the moment.
When we're updating content in Craft, we're frequently clicking 'Save' on categories, entries etc then having the server response timeout on us. The browser says 'Waiting for reply...', but it can take up to 5 minutes for the page to refresh with the saved data, which does appear to eventually being saved correctly.
I've spoken to our hosting company, and they told me that they couldn't see anything unusual in the logs, and advised that I install New Relic to be able investigate the problem further.
I installed the monitoring software along with the PHP service, and added a line at the top of index.php in Craft to identify the individual applications in New Relic.
I've just experienced the problem again on this site, when I was saving a new nested Category.
Going into New Relic transactions, I see in the transaction breakdown for the saveCategory transaction that 300,000 ms was spent in CInlineAction::runWithParams.
I've included the summary trace from NewRelic in the attached image.
Could this is a bug inside Craft, or if there is anything specific to our server which maybe causing this?