Thanks to all of you. Here's a quick summary of the answers I got:

performance problems in a LAMP system

The problem could be located in one or more components:

1. hardware/os
2. apache
3. mysql
4. the application itself

   the usual suspects are the application itself (bad SQL code, inefficient Perl code) and the database (badly laid out database tables on physical spindles)

   hardware/os

   check: CPU utilization, physical RAM/Swap utilization, network bandwidth and disk spindle utilization time.
   tools: vmstat, mpstat, top,...

   apache

   links: Apache Performance Tuning

   mysql

   tools: the mysql slow log, DBIx::Profile
   links: linuxmag article on mysql performance tuning

   the application itself

   tools: Devel::DProf, Apache::DProf

2001-12-13 Edit by Corion : Added missing <OL> tag