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?
I haven't had much of real world experience until recently. I learned coding in school. We started with C then C++ and later C#(.NET) and Java (often in junction with MySQL & Oracle for which we had an extra class also). In between I remember a bit of the ancient arts of COBOL and CICS.
I got into Obj-C when I switched to Mac and tried to get my feet wet with something on my own. Though I created nothing in particular with it.
It's just recently that I started working on a real project (C#) and it's been fun so far and I'm eager to finish it and get onto the next thing.
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?