Two Skinny Kids
Are we in trouble now
Tunnel of Love
I'm sure he can make those last 2 songs sounds great on acoustic as well
Otherwise
Dream of the drowned submariner
Silver Eagle
Devil Baby
Romeo just for you would be awesome too... Hard to choose only 3
I must admit, as a guy who either transcribed or came up with acoustic arrangements of 70 Mark's songs, not every song will work in acoustic, or you need to really work on it hard, sometimes for weeks, trying different variations, tunings and such. Tunnel Of Love will definitely sound dull on acoustic in standard tuning, however, I tried it once in Open G and it actually kind of works.
Mark, of course, has two huge advantages, being the guy who wrote the song and the great singer. He wasn't in the early days, but he developed an amazing singing voice as demonstrated in many of his recent songs. 'Restless Farewell' has perfect singing from MK. The older he gets, the better his voice gets (at least in the studio, I'll not talk about live vocals).