For Punk, you could replace
Dookie with another classic album like
Germ Free Adolescents by Xray Spex, or
Moving Targets by Penetration. You mentioned that your main reasoning for keeping it is because it helped to keep Punk alive in the 1990s. In that case, you could replace it with The Muffs' debut, which came out a year earlier, or
Blonder and Blonder, which came out a year after. In my opinion, The Muffs were just as important to Punk as Green Day were, helping to solidify the Pop Punk sound and to usher in the new generation of punk fans.