The Knights of Malta are an interesting case. There is no doubt that many aspects of their rule were outdated, but they had some good sides and they made serious attempts at modernization. And while they were not terribly popular with the Maltese - indeed, there was even a rebellion in the 1770s - they were not universally hated either. It's telling that the Maltese revolt against the French Republic was way bigger and more popular than this earlier revolt against the Knights.
Henry Sire claims that the Order could have probably saved its domains with a leadership change - as in, if the Grand Master de Rohan died in 1792 instead of being partially paralyzed by his stroke. That way, he could have been replaced by an energetic new Grand Master, instead of muddling along for another couple of years and being replaced by a complete moron at the worst possible time. The fortifications of Malta were not strong enough to withstand any of the Great Powers, if that power wanted to assault it; but they were - Sire thinks - strong enough to make such an assault very costly, so with some clever diplomacy the Knights might have survived to see Napoleon's downfall.
I'm not sure I believe him, but it's an interesting perspective.
There's also the Republic of Ragusa, which I don't think was mentioned in this thread.