I know Blender runs straight out of it's directory after extracting, but I'm a Linux beginner and there are so many different directories in the filesystem, that I have to ask you guys. What is the politically correct place to put Blender 3D 2.69 in the linux filesystem from where I can create a desktop shortcut to?

To install it there are different ways:

From Ubuntu software center, it will probably generate the shortcut.

or type in the terminal:
or
Regards

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I can't really tell you about "politically correct" but if you install something from a package then the executable typically goes in /usr/bin/. If you compile it from source yourself then the executable typically goes in /usr/local/bin. Both of these folders are found in your PATH environment variable. You can confirm this by typing in a console this command:
Otherwise they are usually found or placed in /opt.
As a final point I hope you realise that "politically correct" is an oxymoron.
jdk

Hi. Using the package managers like Ukiuki suggests should ensure updates and less problems, unless Blender like Firefox updates itself but I doubt that... best wishes and have fun.

I manually install 2.69 ( and for needed LEGACY needs i also have 2.49B installed )
" blender-2.69-linux-glibc211-x86_64.tar.bz2 " and the legacy "blender-2.49b-linux-glibc236-py26-x86_64.tar.bz2"

i install NON operating system software in it's own "tree" on a large drive ( not part of the operating system )

then edit or manually create the /etc/applications/???????.desktop file

there are a TON and i do mean A TON of the old python 2 plugins for the OLD api in 2.49b
and still only a few have been ported to the NEW python API in 2.69

running the OLD legacy version takes some system hacking -- not recommended for a NEW user

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