I'm installing a fresh copy of apache and mysql on a windows 2008 server with two hard drives
Primary one is naturally running the OS and more The second drive is for the websites (php scripts)
Where should I install the Mysql and Apache for better performance.
You really won't notice a major performance difference unless you're getting a massive surge of traffic. If so, put it on the disk with the fastest RPM. However, you may want to put all this on the larger disk if you imagine it'll grow beyond the size of the smaller disk.
In general you want the database on a disk that does not have much in the way of other demands on it. with that in mind install Mysql and Apache on the primary and store the database files on the second drive along with the site content.
