I think part of the test of a timeless song is how an acoustic, or 'unplugged' version holds up. When you strip out all the energy and 'noise', do you still have something that you love?
I just saw an old ('75) acoustic performance of Thunder Road (thanks Merlin), and it reminded me of why the song is so great. When you strip it down to its core, it is still amazing.
MTV Unplugged popularized the idea of acoustic versions of rock (and other genres) songs. As a Bon Jovi fan, I've enjoyed a couple Unplugged versions of Living on a Prayer, but the classic one is the '89 MTV Awards:
Acoustic versions often give you a closer and more intimate connection with the lyrics. While this is generally true, and certainly true of the previous two songs, I don't find this Dylan Unplugged version of Like a Rolling Stone creates that closer connection. I think it is too 'busy'. To many instruments, too much noise. Take it as a contrast to the previous two. It is still a great song, but I much prefer the more distilled versions by Bruce and Jon.