I'm finding that a *huge* bottleneck is just parsing the PHP code, before it even gets executed. I have a test page that includes several files, and many of the included files include other files. In total, I have 46 files being included in a page with a total of 32,000 lines of code. Just including these files (before even executing the code) is taking at least .5 seconds. Note that this time does not include the execution of any code, it's just including class definitions, etc., to be used later in the page.
Zoiks! What is it that you're doing, that requires that much code?
Obviously, not including any modules you don't need would help.
I've not tried this, but it would seem that you could make includes conditional on the situations that require them.
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