No kidding. There really aren't "three major opcode caches" anymore, APC won out years ago and is now tightly integrated with PHP compiles and as a module available in any package manager.
It's worth revisiting. We had huge problems with it when we tried it out in 2007, but I tried it again earlier this year and was pleasantly surprised - I got everything working, easily, and nothing broke. And I got that speed up.
My gut feeling tells me that your profiling is correct, however - any significant PHP application (that isn't written terribly inefficiently) will have its bottleneck in data access and not the parse/compile stage. There's very little point to speeding up by 250% a portion of your app that only accounts for 2% of execution time!
