Assuming your sites live in /var/www/sitename and you have the php shell installed in /usr/bin/php you can easily create a cron job that runs all those files.
run
crontab -e
and add this line
42 */12 * * * /usr/bin/php /var/www/*/somedir/index.php >> ~/cronjob.log 2>&1
The * here in /var/www/*/somedir is just a wildcart. This means it will catch every directory in your /var/ww folder.
f.ex:
[jens@localhost ~]$ ls -l temp
total 28
-rw-rw-r--. 1 jens jens 1641 Feb 21 16:12 somefile.py
drwxrwxr-x. 2 jens jens 4096 Feb 22 15:10 test
drwxrwxr-x. 2 jens jens 4096 Feb 22 15:10 test2
drwxrwxr-x. 2 jens jens 4096 Feb 22 15:10 test3
drwxr-xr-x. 8 jens jens 4096 Jan 27 10:21 emptydir
-rw-rw-r--. 1 jens jens 548 Jan 27 16:15 Unsaved Document 1
[jens@localhost ~]$ ls temp/*/testfile.php
temp/test2/testfile.php temp/test3/testfile.php temp/test/testfile.php
As you can see, this returns the testfile.php in each subfolder of temp, namely folder test, test2 and test3.
Emptydir is also a folder, but since it has no testfile.php in it, nothing willhappen with it.
If your directory structure is arbitrarily deep you can use **
e.g.
42 */12 * * * /usr/bin/php /var/www/**/index.php >> ~/cronjob.log 2>&1