I have dozens of favorites. Other than the obvious choices (These Days, Something to Believe In, Dry County, My Guitar Lies Bleeding In My Arms...), I love these:
Silent Night
Incredibly underrated. This particular lyric is perfect in its simplicity, which in my book is a sign of a great lyric
It was all so simple when
You were to be queen and I'd be your king
I guess those dreams got lost
Cause baby you're still you and I'm still me
Bitter Wine
I identified with this lyric for many years
We met some time ago, when we were almost young
It never crossed my mind to ask, where did you come from?
I didn't have much money, so I stole you a rose
You were dressed like an orphan, in Salvation Army clothes
Wedding Day
I tried to make it to the church now, baby
A broken heart got in the way
All I do is tell you I'm sorry
Sorry, I missed your wedding day
Miss Fourth of July
The whole song evokes very strong feelings, it's pure perfection and amazing lyric after amazing lyric. My favorite part is the chorus
So we wave goodbye to Miss Fourth of July
The queen of the roses has left us with nothing but thorns
Don't say we never tried, Miss Fourth of July
The stars that we reached for left us with nothing but dawn
A Teardrop to The Sea
This parts gets me every time (again a very simple but highly evocative lyric)
The laugh of the party, the tears of a clown,
Can't hear a heartbreak, the music's too loud
And I think I Want You and Stay have average lyrics but I like them better than BOR. There I said it
