Check System Calls

strace your web server process
~> /usr/sbin/apache2 -X &
[1] 16367
(hit page a few times to warm up caches)
~> strace -p 16367 -o strace.out
Process 16367 attached - interrupt to quit
(hit page once)
^C
Process 16367 detached

Some common configuration issues you can spot in your strace output:

.htaccess is slow
...
open("/.htaccess", O_RDONLY)            = -1 ENOENT (No such file or directory)
open("/var/.htaccess", O_RDONLY)        = -1 ENOENT (No such file or directory)
open("/var/www/.htaccess", O_RDONLY)    = -1 ENOENT (No such file or directory)
...
In your httpd.conf
 <Directory />
    AllowOverride None
 </Directory>

Finding the Index file
stat64("/var/www/index.html", 0xbfd279ac) = -1 ENOENT (No such file or directory)
stat64("/var/www/index.cgi", 0xbfd27afc) = -1 ENOENT (No such file or directory)
stat64("/var/www/index.pl", 0xbfd27afc) = -1 ENOENT (No such file or directory)
stat64("/var/www/index.php", {st_mode=S_IFREG|0664, st_size=7198, ...}) = 0
Fix DirectoryIndex
<Directory /var/www>
    DirectoryIndex index.php
</Directory>

Watch your include_path
lstat64("/var", {st_mode=S_IFDIR|0755, st_size=4096, ...}) = 0
lstat64("/var/www", {st_mode=S_IFDIR|0755, st_size=4096, ...}) = 0
lstat64("/var/www/foo", {st_mode=S_IFDIR|0755, st_size=4096, ...}) = 0
lstat64("/var/www/foo/PEAR.php", 0xbffcf5fc) = -1 ENOENT (No such file or directory)
open("/var/www/foo/PEAR.php", O_RDONLY) = -1 ENOENT (No such file or directory)
open("/usr/local/lib/php/PEAR.php", O_RDONLY) = 10
open("./something.php", O_RDONLY) = 11
Cause
<?php
ini_set('include_path','.:/usr/local/lib/php');
include_once 'PEAR.php';
include 'something.php';
?>
Fix
<?php
ini_set('include_path','/usr/local/lib/php');
include_once 'PEAR.php';
include './something.php';
?>