You mean shell commands. And the answer is mostly yes. Avoid using shell commands very much, though (it's ok to use mysqldump or mysqlimport for example - they are the same on both *nix and windows). Why do you need them so badly? Write a library in PHP that does the same thing, if it's not a common FS operation or such.
I have optimistic thoughts, even though sometimes (if not always) life's a bitch.