These two parts of the the song remind me of several moments in the House universe. It can be looked at as slash relationship or close friendship. I think these moments were hard on both of them. I cut out the chorus and a verse that go between these two verses because they are the ones that best apply to Wilson and House.

1. This part could work at any time after Amber died and Wilson left PPTH
2. This part works from House's POV after he moved out of the loft in season six, although if you ignore the bit about boxes/ new place it works for Wilson too
3. This bit works when Wilson moved into that hotel in season 2.
4. It can also work for any of the times Wilson has left or been left by his girlfriends/ wives.
and 5. It also works for the time at beginning of season eight/ end of season 7 when House and Wilson are apart even though Wilson didn't move. It would work for Cuddy too since she did move but probably wasn't happy about leaving everything/ everyone behind.

"Got a brand new roof above my head
All the empty boxes thrown away
I rearranged the place
A hundred times today
But the ordering of objects
Couldn't hide what's missing

...Got a big black television set
Now I can watch just what I want
But I'm here staring up
At pictures on the wall
And where are you,
You're still stuck inside them all."


And then later in the song is a lyric that could apply to either of them. It would take place after House bailed Wilson out of jail.

"Got a desk I'll write myself a note
Pretending that it came from you
On hotel stationary
From the time we first met"