Here's a list of the extensions we tend to block on our php file upload system.
1st you would be best to save the files in a none accessible folder that way no one can run any files uploaded and second do a force download of every file, that way it can't be opened either.
Extension list :
bat
exe
cmd
sh
php
pl
cgi
386
dll
com
torrent
js
app
jar
pif
vb
vbscript
wsf
asp
cer
csr
jsp
drv
sys
ade
adp
bas
chm
cpl
crt
csh
fxp
hlp
hta
inf
ins
isp
jse
htaccess
htpasswd
ksh
lnk
mdb
mde
mdt
mdw
msc
msi
msp
mst
ops
pcd
prg
reg
scr
sct
shb
shs
url
vbe
vbs
wsc
wsf
wsh
Also here is a Javascript regular expression of the above:
/(\.|\/)(bat|exe|cmd|sh|php([0-9])?|pl|cgi|386|dll|com|torrent|js|app|jar|pif|vb|vbscript|wsf|asp|cer|csr|jsp|drv|sys|ade|adp|bas|chm|cpl|crt|csh|fxp|hlp|hta|inf|ins|isp|jse|htaccess|htpasswd|ksh|lnk|mdb|mde|mdt|mdw|msc|msi|msp|mst|ops|pcd|prg|reg|scr|sct|shb|shs|url|vbe|vbs|wsc|wsf|wsh)$/i