What guidelines should one follow when customizing their install in order to maintain an upgrade path?

One important factor in making upgrades run smooth is not to do anything which confuses the package manager. That is, you shouldn't yourself touch areas of the system which the package manager expect to be its domain. A few concrete examples.

If you compile/install programs yourself using the ./configure; make; make install method, don't put them directly under /usr. It is better to use /usr/local or /opt, alternatively (even better) to roll your own deb packages.

When you remove packages you can either do a normal removal or an explicit purge. Unless you purge the package the package manager might leave files behind under /etc, /var and so on. Do not delete these files yourself, as the package manager expects them to be there. Instead use your package manager to explicitly purge the remains of the package.

Using deb package from third party repositories should theoretically be safe, assuming they are carefully built etc. Yet, to be on the safe side you might want to consider removing those packages and/or repositories before you perform an upgrade to a new Ubuntu release.

Ok, let me see if I can add some more meat to this answer...

First of all, everything you do in your home directory is perfectly safe in regards to the package manager. It will never touch anything under /home.

(Of course, you can still cause yourself plenty of confusion by doing bad thing to your home directory. Luckily that is usually be recovered from by removing the broken configuration files from your home directory, and let them be re-created from default at the next use. Do note that the automatic re-creation of default config only goes for your personal configuration files, not the system wide stuff under /etc)

In the role of a (power) desktop user I guess the most common system wide creativity will be installing extra applications, libraries, emacs modes, etc? Again, the really important part is to always put none deb package stuff under /usr/local instead of under /usr; to use /usr/local/bin instead of /usr/bin, to use /usr/local/share/emacs/23.1 instead of /usr/share/emacs/23.1 and so on.

Once you start playing around with server daemons you will soon be confronted by the system wide configuration under /etc. While you generally can modify files under /etc, you should "never" actually remove a file or a directory there, unless it was you who created it yourself. Likewise should you be careful about yourself creating new files in there, in case they would later on collide with a configuration file the package manager want to create. That being said, there are definitely files which you can (and should) be created under /etc. On of the more common examples is defining your Apache VirtualHosts under /etc/apache2/sites-available.

There might be times when you want create files or directories under /var. While it is a completely different place than /etc, still consider the same rules about being careful and doing things on individual consideration.

In case you want to know more, it won't hurt you to take a peek at the Filesystem Hierarchy Standard (FHS) or in the Debian Policy Manual. While it might be completely overkill in answering your original question, it is still a good read.