Protecting your secret bits is getting more and more difficult.
IMHO, your solution really depends on your target market. If you are targeting business, just give them the code with a good license, and possibly some type of defect so you can determine who gave your code away if that ever happens. Businesses will mostly pay for your app just to stay compliant; it's not worth the legal hassles. And if an individual gets your app for free, that's probably a good thing, since they will try to convince their current and future employers to buy it.
If you are targeting individuals, and can do it as a web app (which you obviously are with PHP), do it as a hosted service, and either sell a monthly subscription or allow free access and find another way to monetize it.
If you definitely need to or want to distribute it to individuals for whatever reason, you can give it away for free, and try to monetize customizations, add-ins, & other support features.
This is a problem that's been discussed a lot, and a few hours’ worth of really focused googling should reveal all the current philosophies on this.
I hope this helps.