Why doesn't The Doctor call himself John Smith anymore?

The same reason he doesn't use Psychic Paper anymore
The same reason no previous Doctor's (except David Tennant) are coming back for the 50th
The same reason no previous companions (except Billie Piper) are coming back for the 50th
The same reason Clara is The Rani/Romana/Susan/Jenny
The show is doesn't care about it's history

Possibly because Matt's surname is Smith and it would be too much of an in-joke.

Hmmm has Matt Smith ever used psychic paper before?

I'm pretty sure he has.

because the Doctor tends to use that name when he goes undercover,and doesn't want people to know who he is

I was thinking the same, but i'm having a brain fart and can't think of a single moment....

im sure he used it in the Eleventh Hour

Didn't he use in in the Vampires of Venice to get into the school. Rory ended up having to be a eunoch.

Did you spot the key in tonight's episode with "Smiths" on it?

A Christmas Carol

Vampires of Venice (or tried to at least but showed his Library card)

Yes, he did. And actually 'John Smith' also made an appearance in that episode. When the Doctor was trying to pull out the psychic paper when faced with a bunch of the 'vampires' he pulled his library card instead, which had a picture of the 1st Doctor and the name 'John Smith' on it.

He flashed it in Hide.

Ahhh yes thanks guys!!!