This still eludes me.

Regardless of distribution (although perhaps it can't be disregarded altogether), where do I put my application files?

For example: I download DoFoo.tar.gz. Where is a sensible place to:

1) store the .gz

2) extract the files to

3) install the app?

And why is it sensible? I'm looking more to understand how linux works and what the implications are of keeping files in this directory or that.

I guess I would make the assumption that I am using a Debian based distro and am currently the only user, but that other users might be added who would want to use DoFoo for all its amazing features.

Help me understand this linux thing (2 years after I've started using it).

Thanks.

Probably /usr/bin, a quick googling...
http://www.freeos.com/articles/3102/

Have you ever looked at the Filesystem Hierarchy Standard? It will provide you the rationale for what goes where.

Thanks for the links. I've scrolled through these but I'm still a bit fuzzy. In the above example, where would you put each of the 3 items?

Download and unzip in your home directory would be ok - as said above, probably install to usr/bin but depends what it is.
The zip and extracted files will generally be deleted so home directory is ok.
Read the link weibullguy posted again - these guys recommend the file system layout with reasoning....eg. /usr/bin: Most user commands

Source code usually goes in /usr/src but it doesn't really matter, you can keep all the files in your home directory if you want

I have recompiled my kernel twice, and installed from source maybe three times, so I am hardly an expert, but the way I understand it is this:

You can download the tar file anywhere that is convenient.
You untar it, and cd to that directory.
./configure configures it
make does the make bit
(as root) make install installs it, wherever it is "supposed to go", and this is probably determined by the previous two steps.
Thereafter you can delete the source directory, as it has had its use, although I tend to keep them as the READMEs can be useful later.

Edit: You are using Debian, why don't you just use apt-get, or one of the graphical repository managers to install software? /Edit

Thanks for the info.

Naturally because it isn't found in the repository.

I think /usr/local is the most common destination for ./configure, make, make install stuff.

Source should be /usr/src according to FHS

/usr/local is the default prefix if the package uses GNU autotools but it might be somewhere else if not. /usr/src is for storing source code for reference purposes, it's not supposed to be used to build software.