Sorry if this is a stupid question but I've never read any of the books.

i have a number of neutral cards each with one of the following traits :

Brotherhood

Kingsguard

Night watch

Wildling

Although I believe that i am allowed to include these in any deck i was wondering, based on the books, which of the Houses these cards would sit most comfortably with.

Based on the books? (Warning, Spoilers) Creating decks to fit the books is what we call "Nedly" behaviour - it doesn't always make for a very competitive deck.

The Kingsguard in the books are guarding primarily Joffrey Baratheon and then Tommen Baratheon. All the new appointments are made by Lannisters, so that'd probably be your best bet.

The Night's Watch stands apart, so "should" be neutral, but of all the houses it receives the most support from Stark, who are near enough to the wall to understand the value of keeping it manned. I'd say Stark.

Wildlings should definitely be neutral house - they have allegiance to no house.

The Brotherhood without banners started as appointed by Ned Stark, then hand of the king, on behalf of Robert Baratheon to hunt down Clegane, a "renegade" Lannister. They could reasonably be run out of Baratheon or Stark and fit the lore quite well. They do drift from their original mission, and for all intents and purposes become neutral.