The Dock is used to launch and switch between applications.
My 120 billion byte hard disk is using only 24 billion bytes (so far). According to the Disk Utility app, it has 164 thousand folders and 700 thousand files. I am the only account on the system.
Certainly some folders and files are more important than others. The Eighty-Twenty Rule applies.
80 to 90 percent of the work you do is done by 10 to 20 percent of the applications you use.
The left side of the Dock is for immediate one-click access to those indispensable most-used applications.
The first item is everyone's most used application: the Finder.
This is followed by other indispensable applications for which you want one-click access.
The right side of the Dock is for folders and minimized documents. Folders contain any of applications, documents, and folders.
The Dock in Leopard comes installed with two folders: Documents and Downloads. Use them to keep the desktop clear.
Folders in the Dock are transparent: you can see what are inside them.
Spaces is used to create and manage multiple virtual desktops and display them in an Exposé-like interface.
Spaces gives you 4, 6, 8, 9, 12, or 16 desktop spaces. An application can be assigned to any one of these. Or assigned to every one. Or assigned to none. This is done in System Preferences > Spaces.
(i have set the first four applications in the dock to spaces 1 through 4.)
Control-n for n from 1 to 9 is a convenient way to switch you to Space n. Set this in System Preferences. You can also switch spaces with ⌃← and ⌃→.
Clicking on Spaces in the Dock shows what's in each space. You can use Exposé to separate items in the spaces. Items can be dragged from one space to another. This let's you have more than one space for items in an application.
My Current Dock 
Mac OS X Public Beta, 2000 