Well first it will be a complex job in my view.
The http://www.minecraftwiki.net/images/0/01/Skinzones.png file you mentioned is flat, but you have to convert that in ISOMETRIC 3D look, so you have to distort the images
For example look at the images below
So you can see that 3D box image is created from the pieces of other images, the logic is to add perspective to the flat images and join them. but as it is 2D we will call it Image Distortion.
Unfortunately GD Library which comes bundled with PHP is not advanced enough to let you do such things.
You have to use some other library like Image Magic and this link is tutorial for using distort functions http://www.imagemagick.org/Usage/distorts/
Second big thing is the processing of the images, you can process the images live but it will consume lots of resources on server, so it is suggested that you use pre processed images, and not process them every time.
To generate the Isometric image you have to write the code your self, and it may need alteration on each image character depending upon the size of the image. But when you have written a code it will be easy.
My Suggestion is to write your own code once, then alter it for every character and save the processed images in a sprite and use them when you add play functionality.
check out this link as well
http://www.fmwconcepts.com/imagemagick/index.php