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PHP I picked up entirely from a shopping cart system on devshed.com
I learnt JS from Thau's legendary tutorial on webmonkey.com.
'Sams Teach yourself how to build Web Pages' - for the HTML.
'Sams Teach yourself PHP in 24 hours' - for, you guessed it, PHP.
'Sams Teach yourself JavaScript in 24 hours' - for JavaScript.
However, there are quite a few online tutorials which are free. But I've always prefered paper-back rather than screen reading. The HTML book is pretty out-dated, and I'd look into HTML 4.01/xHTML 1.0 nowadays.