Good God, this is incredibly hard to do! I will give you that Aenema is a great song, but one of the best ones I've heard by Tool is Eulogy. Stinkfist and Hooker With a Penis also rock my world. I love Tool... /fangirl
Others I can think of off the top of my head:
Immortality -- Pearl Jam
Love, Hate, Love, Down In a Hole -- Alice In Chains
Say Hello to Heaven -- Temple of the Dog
Birth Ritual, Seasons -- Soundgarden
Nirvana -- Something (in the way)
Minister/Medicine Woman -- Floater
Magdalena, Thinking of You, Pet -- A Perfect Circle