Ive just had a hugh transformation on a e-com site from Linux to a Win32 platform (dont ask me why) . The problem that I had with in this was, connecting to MsSql, and php.ini settings. There was not much need for to change the source code except for connection, queries extra.
The php.ini file, I had to turn on globals and turn down the error reporting a noch or two. Also had to setup the remote connection to MS SQL
Im currently working on the securitiy on the site...to have the globals turn off among others.
So this is more of a visa versa to you question...but Im sure it will help you narrow down your problems that you might occur