Finding an ideal directory structure

My recent forays into coding have left me with some pretty confusing directory structures. I tend to break up my directories thusly: (I'm talking about web dev for the time being)

[myProj] - project
    [scr] - scripts
        [php and javascript files that store functionality]
    [mod] - modules
        [php scripts that will be include()d and rendered on the page]
    [img] - images
        [pictures and such]
    [css] - style
        [css files]

An avid onlooker would notice that where I can, I name my folders a three letter abbreviation of their full name. This is because I am lazy.

As my projects become more intense I am finding this to be a bit inadequate. I am beginning to wonder if there is a scalable solution? How do you analyse a directory structure to the point that you can determine if it is "good'? I assume this is a common problem so there must be many solutions.

For instance I have my lazy.js file which I like to use across all the sites I host (of which there are a few) and I don't want to have to keep copying it into each site directory. So I employed a "common" folder.

[www] - base folder
    [si1] - site 1
        [scr]
        [mod]
        [img]
        [css]
    [si2] - site 2
        [scr]
        - you get the picture
    [com] - common folder holding mysql connection script, lazy.js/php etc

But I am wondering if this will scale well as my projects become even more complex. When I move back into Java and other compiled languages I'll have to trial-and-error my way back to a nice directory structure all over again. For web design I can include a file with an absolute path, but for compiled code how can you do that? Do you need to do that?.

So I ask all three of the people who very kindly follow this blog, what directory structures do you use? Have you figured out a way to ease the pain of multiple file includes and maintenance of? Got any resources you feel like sharing? Hit me with it yo.