The best way to learn notes is to sing them as you play them*. Say you play a C, just sing in pitch with your guitar. For some reason, this method will implant the sound of the C in your mind very naturally. And just go on til you learn all 12. Josh, I see you said that you knew the sound of the important ones, well why not just learn them all. If you can learn a few of them, you can learn them all.
*Note: Play notes around the middle C range, the pitches are much easier to hear in this spectrum. As you go lower they become muddy (bass players know what I mean), and the higher you go the more fragile and tinted they become.
This is still not Perfect Pitch, cause that is a far broader range of perception. This is just what most people are really after, and it's a invaluable skill to know all 12 notes.
Also, just another note here is a small list just off the top of my head of people who have Perfect pitch: Frank Sinatra, B.B King, Miles Davis, Tommy Mars, Eric Johnson, Yngwie Malmsteen and countless classical musicians.
"My whole life is a dark room...ONE BIG DARK ROOM" - a.f.i.