<p>What is the recommended practice? Should I add the my sub-folder under the fitnesse folder to version control?    </p>

<p><em>Context: working on a single developer rails pet project. I've my rails project under version-control (Subversion) however my fitnesse wiki pages lie under the fitnesse program folder.</em></p>

<p>Fitnesse seems to have its own version-control... (I see numbered zips along with each of my wiki pages) Is it reliable? Where does it store the revisions?</p>

FitNesse stores old revisions of every page in a zip file in the same directory as the page's files. The zip filename marks the timestamp of the revision. It works similar to wikipedia - history, but not full-fledged version control.
In our company we wanted a setup where whenever we checkout a (possibly old) revision of the source, we also check out FitNesse tests that pass for that specific version.
Therefore, we installed FitNesse (the fitnesse directory, including the FitNesse executable and the FitNesseRoot directory) inside our source tree in version control, setting a rule to not import *.zip within the FitNesseRoot directory (as we have version control to keep history for us and don't need them).
This works excellent with sane SCMs (I used svn w/ svn-tortoise).
When we moved to Microsoft Foundation Server source control we had many issues with the checkout-edit-checkin workflow. Then again, this workflow is simply a bad idea in general, and should only be used by insane control-freaks.
(edit: answered commenter's question)