That's really a tough question in a lot of ways, since the eras were so vastly different.
There are a boatload of shows I remember fondly from the 80s (my generation) and still like today: Godzilla, Dungeons & Dragons, GI JOE, Transformers, He-Man, et al
The 90s were a more diverse group, with a lot of Media tie-ins: Tiny Toons Adventures, X-Men, Spider-Man, Exo-Squad, the origins of the "DC Timm-verse", and who can forget classics like Duck Tales, Chip & Dale's Rescue Rangers, Tale Spin, and Darkwing Duck? Love em all...
Frankly, the 2000s, while producing many gems, such as Dexter's Lab, Johnny Bravo, X-Men Evolution, and the continuation of the "DC Timm-verse", saw them often drowned out by the flood of CCG based POKE-YUGEH-MON-OH crap. One bright spot has been the introduction of the mass DTV, working outside the newly re-tightened S&P censors, giving us the Lionsgate Marvel Projects, Superman/Doomsday, et al.
For me, it isn't about "generation", it's about what's GOOD...and that is becoming increasingly harder to find, starting in the early 00s, because the nets are aiming for the "lowest common denominator" with animation in general.