See our SD Thicket PHP Obfuscator for an obfuscator that works just fine with arbitrarily large sets of pages. It operates primarily by scrambling identifier names. With modest to large applications, this can make the code extremely difficult to understand, which is the entire purpose.
It doesn't waste any energy on "eval(decode(encodedprogramcode))" schemes, which a lot of PHP "obfuscators" do [these are "encoder"s, not "obfuscator"s], because any clod can find that call and execute the eval-decode himself and get the decoded code.
It uses a language-precise parser to process the PHP; it will tell you if your program is syntactically invalid. More importantly, it knows the whole language precisely; it won't get lost or confused, and it won't break your code (other that what happens if you obfuscate "incorrectly", e.g., fail to identify the public API of the code correctly).
Yes, it obfuscates identifiers identically across pages; if it didn't do that, the result wouldn't work.
