Well, despite the fact he was a tactical genius and politically very astute, a lot of his organizational capability comes from his chief of staff, Berthier, who was able to not only stay up for days on end without sleep relaying Napoleon’s order but was also able to “read his mind”, being a military man himself, and translate Napoleon’s general instructions into more detailed ones.
Well, he commissioned the creation of the Code Napoleon, which is still the basis of law in some parts of the world (as opposed to English common law.)
He caused the final collapse of the Holy Roman Empire after the war with Prussia in 1807, with unknown subsequent affects on Germany in the latter part of the 19th century. (I.e. if he hadnt given the final push, who knows how long before Prussia could finally become Germany?)
As well, and this is probably more of an early Republic thing than a Napoleonic thing, but when the French armies invaded Western Germany and Italy they would often help destroy the remnants of the old monarchical states and institute a more republican-friendly regime. These were done away with after France was defeated, but perhaps the taste of more liberty accelerated the revolutions throughout Europe in the latter part of the 19th century.
In addition, the Napoleonic wars themselves influenced the nature of warfare for the next 50 years. Despite the fact that armored cavalry was on the wane, Napoleon’s cuirassiers did so well versus other, less armored, enemies, that other nations tried to emulate them (I’m not sure when they realized their mistake, but I’m sure it happened right around the same time rifled muskets became popular, putting the final death knell into the age when hand-to-hand combat would regularly decide the outcome of battles.)
In addition, an officer serving with Russia write a little book on tactics that the United States used as part of its officer training regime. Many officers in the American Civil War were influenced by Jomini, for good or ill (mainly for ill, but they were probably not worse of than if they followed another randomly out-of-date manual rather than common sense formations. I’m pulling that out of my posterior, though, so take that with a grain of salt)