Oh I was about to create a very similar topic so I'm glad I found this!
Here's what my site looks like:

I get pretty passionate about organizing stuff.. So allow me to explain how my site is organized!
First off, I have all the main pages sitting in the main folder, and if they have an individual style-sheet I just name it the same way but with "-style" at the end! However several pages use a generic stylesheet, that I (creatively) named "generic-page_style"!
I also have a stylesheet called "color-pallete". This style sheet contains all the root variables I use in the "generic" pages! It's on a separate stylesheet so it's easier to switch it out for a totally different color scheme. Right now I'm planning on having different color schemes that change based on the seasons (or depending on the day cycle! haven't decided yet) and automating it with javascript. Having all the colors being on a separate stylesheet is gonna make that super easy!

I've also considering doing a drop down menu that lets users can choose the color scheme they like the most.
Anyways! When I do make more color palletes I'll probably make a dedicated folder for them.
I use a folder called "widgets" for all the little files for... well, widgets! It's stuff like javascript files a stylesheets for music players or similar doodads! This is one of the latest additions so it still needs some stuff moved into it.
I have an HTML file for my navbar. I was tired of having to update it on every page every time I added something new to the site, so right now I use an iframe for it. This way I only have to edit it once! But it takes a bit longer to load :P Anyways! The navbar html file will go in the widget folder eventually, but I have been lazy to move it.
The "homepage_iframe" folder (containing html files for an iframe in the homepage) is also waiting to be moved in the widgets folder right now
All the "secondary" HTML pages go in their little dedicated folders, like "collections" and "blog_entries"
And I also have a dedicated folder for all my RSS feeds!!
Last and DEFINETLY least.. we have the only thing I hate about my site organization: the "assets" folders. YES. FOLDERS PLURAL. Unfortunately I got distracted and forgot file names are case sensitive!

I ended up creating two "assets" folder (one with an upper case a and the other with a lowercase a) on accident. When I finally noticed, most of my assets were in the lowercase one, with only a couple of images being in the uppercase folder. Unfortunately, one of that couple of images was my site button!

Now I cannot remove the folder without breaking all of my buttons on sites linking back to me!! So I'll have to live with two assets folders FOREVER!!
Anyways.. sorry for the long rant!! I get really passionate about this stuff