wow, a thread actually about music...refreshing.
-Transcribing music. Figure out (and write down notation if possible) some bass lines, horn parts, vocal melodies by ear. You can always consult sheet music to see how close you came by ear, and then learn from the transcribed music where you went wrong. Don't jump right in to Matt Garrison/Malmsteen/Coltrane solos, something simple but relevant like U2 or The Meters basslines are a great place to start, or whatever you're digging.
-Solfege. The old Do-Re-Mi. Learn to sing written notaion using this method. There are tons of great books out there on how to learn this. Get some kind of cheapo keyboard or a keyboard app. it'll help.
-Sing. Sing what you play. I find this always helps me internalize any line, lick, or riff, and to own it as music rather than just a series of hand movements. And for the record, my singing voice sounds pretty awful, but that's not really the point, just try to sing it accurately and in tune.
-Listen. Take time to just listen very carefully to music, and not immediately try to figure it out. Take entire passes of listening to a song and focus on one instrument all the way through. Focus on the the contour of melodies, different uses of rhyhtm in the instruments, and the chords and arrangement. Really "go micro" on the piece of music.