You should see if you can post or search the export features on the Journler forums for the best answer:
http://journler.com/community/forums/index.php
You're right though, no software is ever going to be fully future proof from OS upgrades or any number of unforeseen events. I would never fully trust any one application or computer platform for that matter with information you intend to keep for years or decades.
Personally, I use Evernote, and for my 'critical' information, this is how I handle it:
1. Save each item as .txt file (copy / paste if no export is available). I don't worry about the formatting... this can be handled later if needed. Only the content is truly important. Something like TXT will be readable by some application on any platform, past, present or future in our lifetime (and probably beyond).
2. Print a copy to paper and put it in a binder. These copies can always be scanned and use OCR to translate back to workable text. Worst case, type it out again.
Don't count on Journler lasting more than a few years or being able to run it. Very few things do. I don't know that I would trust Word or PDF compatibility either over the long haul.
Good luck -
Wayne