LA - the best part of LA is Venice / Santa Monica, so stay at somewhere like the Cadillac Hotel on Venice Beach. Also, get the fuck out of LA, hit up the SixFlags, hit up Santa Barbara, check out San Diego and Long Beach.

San Fran, unless you want shopping, stay in Haight-Ashbury, and avoid Downtown / Union Sq. Get out, go visit the giant redwoods or the wine districts.

NYC - there's interesting shit in all the main areas, but don't discount Brooklyn as a place to base yourself. You'll probably have a better time at night in their bars than you would in midtown for example. Also, get the fuck out and go visit Atlantic City and the Jersey Shore, go spend a couple of nights in Philly - catch the Amtrack.
Hopped in the car and torpe'ed to the shack
Of Shaheed, "We gotta go back" when he said
"Why?" I said, "We gotta go
'Cause I left my wallet in El Segundo"