exec           - Returns last line of commands output
passthru       - Passes commands output directly to the browser
system         - Passes commands output directly to the browser and returns last line
shell_exec     - Returns commands output
`` (backticks) - Same as shell_exec()
popen          - Opens read or write pipe to process of a command
proc_open      - Similar to popen() but greater degree of control
pcntl_exec     - Executes a program

eval()
assert()  - identical to eval()
preg_replace('/.*/e',...) - /e does an eval() on the match
create_function()
include()
include_once()
require()
require_once()
$_GET['func_name']($_GET['argument']);
$func = new ReflectionFunction($_GET['func_name']); $func->invoke(); or $func->invokeArgs(array());

Function                     => Position of callback arguments
'ob_start'                   =>  0,
'array_diff_uassoc'          => -1,
'array_diff_ukey'            => -1,
'array_filter'               =>  1,
'array_intersect_uassoc'     => -1,
'array_intersect_ukey'       => -1,
'array_map'                  =>  0,
'array_reduce'               =>  1,
'array_udiff_assoc'          => -1,
'array_udiff_uassoc'         => array(-1, -2),
'array_udiff'                => -1,
'array_uintersect_assoc'     => -1,
'array_uintersect_uassoc'    => array(-1, -2),
'array_uintersect'           => -1,
'array_walk_recursive'       =>  1,
'array_walk'                 =>  1,
'assert_options'             =>  1,
'uasort'                     =>  1,
'uksort'                     =>  1,
'usort'                      =>  1,
'preg_replace_callback'      =>  1,
'spl_autoload_register'      =>  0,
'iterator_apply'             =>  1,
'call_user_func'             =>  0,
'call_user_func_array'       =>  0,
'register_shutdown_function' =>  0,
'register_tick_function'     =>  0,
'set_error_handler'          =>  0,
'set_exception_handler'      =>  0,
'session_set_save_handler'   => array(0, 1, 2, 3, 4, 5),
'sqlite_create_aggregate'    => array(2, 3),
'sqlite_create_function'     =>  2,

phpinfo
posix_mkfifo
posix_getlogin
posix_ttyname
getenv
get_current_user
proc_get_status
get_cfg_var
disk_free_space
disk_total_space
diskfreespace
getcwd
getlastmo
getmygid
getmyinode
getmypid
getmyuid

extract - Opens the door for register_globals attacks (see study in scarlet).
parse_str -  works like extract if only one argument is given.  
putenv
ini_set
mail - has CRLF injection in the 3rd parameter, opens the door for spam. 
header - on old systems CRLF injection could be used for xss or other purposes, now it is still a problem if they do a header("location: ..."); and they do not die();. The script keeps executing after a call to header(), and will still print output normally. This is nasty if you are trying to protect an administrative area. 
proc_nice
proc_terminate
proc_close
pfsockopen
fsockopen
apache_child_terminate
posix_kill
posix_mkfifo
posix_setpgid
posix_setsid
posix_setuid

// open filesystem handler
fopen
tmpfile
bzopen
gzopen
SplFileObject->__construct
// write to filesystem (partially in combination with reading)
chgrp
chmod
chown
copy
file_put_contents
lchgrp
lchown
link
mkdir
move_uploaded_file
rename
rmdir
symlink
tempnam
touch
unlink
imagepng   - 2nd parameter is a path.
imagewbmp  - 2nd parameter is a path. 
image2wbmp - 2nd parameter is a path. 
imagejpeg  - 2nd parameter is a path.
imagexbm   - 2nd parameter is a path.
imagegif   - 2nd parameter is a path.
imagegd    - 2nd parameter is a path.
imagegd2   - 2nd parameter is a path.
iptcembed
ftp_get
ftp_nb_get