For PHP: PHP and MySQL Web Development, 4th Edition by Welling and Thomson. Learn about PDO and parameterized queries and such from the online docs; the book treats security poorly. The Web Application Hacker's Handbook would probably be a nice third book if you're feeling indulgent.

For JS: JavaScript: The Definitive Guide, 5th Edition by Flanagan. Until Secrets of the JS Ninja (or the Rhino book's 6th edition) comes out, then get those.

Out of curiosity, what have you worked with previously?