As hessian already said Google will index .php files. However it has a big problem indexing dynamic pages, esp. those that work like this:
index.php?site=3 - say this is "news"
index.php?site=6 - this is another part of the page
Google will index the index.php only once, for whatever reason. There is a solution to this though. Mail me if you're interested in knowing more.
Greets,
Dominique