Although I have never created a commerical script to sell to multiple clients, I am a PHP developer and there are several ways you could accomplish this:
Zend Encoder (which was already mentioned) is the most expensive, but also the fastest and compatible with the vast majority of web servers with PHP (since the "decoder" is the free Zend Engine, found on standard PHP installations). It's the nicest product since the top folks at Zend are the founders of PHP.
IonCube Encoder is very similar to Zend's product. Although it's less expensive, it's much less compatible with most servers because it's not on the standard installation. You need a server admin to install the IonCube loader, so you really cut your number of potential clients down. Even if they do have the loader, they might get confused/frustrated and choose a competitor's script.
Keep in mind with either Zend or IonCube, most developers only encode their "core" functions/processes, so it allows the end-user to edit/mod the code without being able to easily replicate the backend. The pluses to these is to the best of my knowledge, they've never been cracked and won't be soon.
Other solutions:
You could add a "phone home" portion to your script that sends a XML-RPC message or something of the sort. Just make sure you turn error-checking off in case someone's using your script on localhost, etc. Then you can manually see the site and make sure the license checks up with your database of users.
You can make parts of your "core" almost unreadable by man (it makes it look like gibberish and would make it difficult to mod). There are free programs out there that will do this for you. Although your users might not appreciate this.
In conclusion, people who have every intent of buying your script will and everyone who doesn't or won't pay to use it will either try to crack it or give up and use something else. Either way, it doesn't really matter - you're not getting the money. So, it's usually best not to make the encoding/licensing your primary concern. Focus on your clients, they've got the money, not the kiddies.