thats a tough question. i couldnt limit it to 12 to represent the whole century, but i will list some that i think should go in a time capsule. this is by far not complete, but should give a descent representation of the century:

miles davis - kind of blue
orson welles - war of the worlds (live radio broadcast)
jimi hendrix - are you experienced (and electric ladyland)
james brown - love, power, peace
muddy waters - The Anthology: 1947-1972
nirvana - nevermind
micheal jackson - thriller (and off the wall)
beach boys - pet sounds
johnny cash - at folsum prison
the misfits - walk among us
paul oakenfold - voyage into trance
pink floyd - dark side of the moon
george gershwin - rhapsody in blue
radiohead - kid a (and ok computer)
bill monroe - the essential bill monroe & his blue grass boys
robert johnson - complete recordings
nine inch nails - the fragile (and the downward spiral)
ella fitzgerald and louis armstrong - porgy and bess
pearl jam - ten
aretha franklin - aretha live at fillmore west
john coltrane - blue trane
hank williams sr. - the complete hank williams
woody guthrie - the greatest songs of woody guthrie
rodgers & hammerstein - the sound of music
bjork - homogenic (and post)