In some cases there are games that the publisher says are unavailable but that retailers still have plenty of copies available, like Star Wars: Rebellion. In that case, the publisher probably has another print run in work, so the game is likely to remain available for the foreseeable future. My focus here is on games that can't generally be found in normal retail channels because the publisher has not maintained it in production or distribution.
I had expected to include Mechs vs. Minions on this list as a Kickstarter-only release, but I have come to learn that Riot Games has made it available for direct purchase and in fact is in their third printing.
A special case is Android: Netrunner, a living card game from 2012 that Fantasy Flight retooled in a "revised edition" last year but which has been discontinued due to a license agreement with Wizards of the Coast that was not renewed. The core set remains available in retail for the time being.
So here are the top five bgg-ranked games that appear to be unavailable through retail or direct purchase:
#14. The 7th Continent (designers Ludovic Roudy and Bruno Sautter, artist Ludovic Roudy, publisher Serious Poulp): The publisher released it for Kickstarter backers only in 2017, and conducted a second Kickstarter campaign, but never intended it for normal retail distribution.
#32. Through the Ages: A Story of Civilization (designer Vlaada Chvatil, artists Richard Cortes and Paul Niemeyer, publishers Czech Board Games and Eagle-Gryphon Games): This 2006 release has been supplanted by Through the Ages: A New Story of Civilization, which is ranked #3 on bgg at this writing. A few copies of the original can still be found on Amazon at what appear to be after-market prices.
Eclipse (designer Touko Tahkokallio, artists Ossi Hiekkala and Sampo Sikiö, publisher Lautopelit.fi): This 2011 game's last English edition was released in 2015 and appears unavailable except on Amazon at a significant premium. Next spring, Lautapelit.fi will release a reimplemention as Eclipse: Second Dawn of the Galaxy.
#48. Twilight Imperium: Third Edition (designer Christian T. Peterson; Artists Scott Schomburg, Brian Schomburg, and Tyler Walpol; publisher Fantasy Flight): This 2005 game has been supplanted by a Fourth Edition, which is ranked #17 on bgg now.
El Grande (designers Wolfgang Kramer and Robert Ulrich, artist Doris Matthäus, publisher Rio Grande): This game was #21 on bgg when it appeared on my list of unavailable games four years ago. The English-language 1996 edition has not been carried by Rio Grande for some time. Rather, Z-man in 2015 released an El Grande Big Box that includes the core game along with six expansions.
The last time I compiled a list like this, four of the five titles had no prospects for follow-ons. Only one - Command and Colors: Ancients - was a candidate for re-print as part of GMT Games's P500 program, and it did in fact see a 2014 fifth edition release. This time, most of the titles listed had some kind of follow-on that rendered the original obsolete. Even the one Kickstarter-only title had - or will have - a second release in the form of another Kickstarter campaign fulfillment.
So there has been something of an evolution in the game market that seems to keep the highest-rated titles available in one form or another, which is, I suppose, as it should be.