What I'm wondering is if I copy the /usr, /etc, /lib, /opt, /var, /boot, etc. directories from one machine, install Linux on another machine and override those directories with these directories will my system function correctly. I'm trying to find a quick way to setup Linux boxes on different hardware and I was wondering if there's a trick I can use to set up one system, configure it, install all the updates, install new programs, and copy the information to another system. Since Linux keeps things pretty well sectioned off I thought with the exception of a few files like XF86Config-4 providing I provide the same files all programs should function accordingly? Is this feasible?

I have been known to copy the /home/username folder over to other machines but, you may not get away with copying the basic system folders.
Maybe you would have better success with the super cool program called clonezilla. It's designed for getting a system setup the way you want it then, putting that image onto a server. From there, you can boot thin/thick clients. Or, you can use it to grab the image and put it onto the client machine.

Check it out!!

DRBL (Diskless Remote Boot in Linux) / Clonezilla / Partimage / Freedos
http://drbl.sf.net