Performance troubleshooting relies upon comparison. To know that performance is bad, you must have a preexisting benchmark from when performance was good. Though we can continue giving hundreds of examples of performance-related issues, a better approach is to understand the tools and know what to focus on.
To solve storage-related performance problems, you must be familiar with common tools such as sar and iostat. For threaded applications, make sure your version of top shows threads. Otherwise, focus on the ps command with the m flag. Other performance monitoring tools exist, such as Oprofile, Prospect, q-tools (q-syscollect, q-view, and q-dot), Perfmon, and Caliper.