How to debug WordPress correctly?

I’m using a few plugins and UpThemes framework on my new website and if I turn on Wp Debug I can see that there are a few errors related to Deprecated functions (but website is working). What I would like to know is if there is a plugin, a software or a pray (lol) that I can use to know exactly where the deprecated code is so I’ll be able to use the new one.

Which is the plugin/software that you use to debug your plugins, themes?

What you’re looking for is the Log Deprecated Notices plugin. (Don’t run it on a production site, as it is a direct-to-database log.)

What it’ll do is convert those cryptic messages that are likely to reference has_cap() or some line in functions.php, to what’s actually going on.

The Debug Bar plugin is also nice. It tracks notices of that pageload, using the conversion code from Log Deprecated Notices.