You know the gen 4 to 5 is an obvious answer, but I think age is playing a role here as is our knee jerk vote... When I really think it over the leap from Gen 2 to Gen 3 is clearly the bigger one. They didn't add a dimension but the leap in scope was far larger going from those earliest of consoles to the NES/SMS etc days, saved games were popularized, the modern controller was born, and I see a greater graphical difference between Pitfall and Super Mario Bros 3 than between a Super Mario World and Super Mario 64. Sports games also made the transition from largely unestablished franchises into more popular ones, such as Madden.
Heck, most of the games from the 2nd gen were just one screen, had exceedingly simple sound effects, and had such limited graphics that you required a manual just to know what each square represented. The difference is certainly larger in my opinion... Those gen 3 games have always seemed to me to be the clear birth of the modern industry, whereas gen 5 was simply embracing and running with the 3d that had been attempted and toyed with on gen 4.
Also, Gen 2 saw cartrige-based handhelds get off the ground.
