The Devel module offers database logging to check whether you have any long running queries.
If this doesn't help take either XHProf or XDebug and find the guilty code. XHProf (a profiler) draws you a nice map of all the functions that are being executed on the server, and it tells you which ones are consuming the most execution time to execute. On the other hand, when XDebug (a debugger) is configured with an IDE such as Eclipse (see video) it allows you drill down into every function being executed LIVE. The profiler will give you an idea of what is being executed; while the debugger will show you why is it being executed.
