I think it is most important to just be consistant. Thery are just guesses anyway.
I always use Rager for my IBU calculations. If get a recipe that is done in Tinseth, that is fine, I enter it into my software, and calculate the IBUs from the Rager formula. That is how many IBUs are "in my beer."
So the next time I go to brew, if want about the same bitterness, I shoot for the same IBUs as that recipe, or adjust from there.
I guess most homebrewers use Tinseth, but I guess Rager is what my software defaulted to. http://www.homebrewtalk.com/f84/tinseth-rager-garetz-ibu-calculations-40296/