Well, there is not a definite 'best' but rather which suits your needs.
Eventhough I would have to say MySQL all the way, why? Cross-platform... And also the fact that administration interfaces like phpMyAdmin work through a normal browser.
I dont see a real advantage for MsSQL over MySQL, I would dare to say that MsSQL is slower sometimes. MsSQL's strength lies within the tight integration into MS dev environments and the DB driver models.
So yeah, as long as you're going php, MySQL and you wont have to worry about which platform it may run on.