Two that I always thing of:
It Ends Tonight - All American Rejects
Kiss From a Rose - Seal

I'm sure those songs have meaning for those artists, but either I don't completely understand them, or can't relate to them (Yes I know KFAR is probably about drugs)
But the music in those songs is so hauntingly beautiful, that I still consider them some of my favorites

IMO there are such a small percentage of songs that combine great music and lyrics...