It's Series 31 or 1, not 5 says Steven Moffat
In a recent DWIN blog post, it quotes Steven Moffat, new series Executive Producer and Lead Writer for Doctor Who speaking of the upcoming series for the year 2010 (Matt Smith's first series as the 11th Doctor) in the latest issue of Doctor Who Monthly magazine:
"It’s Series Thirty-One of Doctor Who, and it's Series One of Matt Smith's Doctor, Those are both real numbers. I submit that 'Series Five of Doctor Who' means absolutely nothing unless you really believe that Matt Smith is the third Doctor. Everyone knows he's the Eleventh Doctor so that means it’s definitely not 'Series Five'. Whichever number you choose, 'Series Five' is the one that's flawed."
"'Series One' is an exciting sentence. 'Series Thirty-One' is an awe-inspiring sentence. 'Series Five' is a boring sentence - and also a complete lie."
The blog post also reports of unconfirmed talk that the DVD sets and other merchandise will be branded as 'Doctor 11, Series 1.'
So let the debate end, or simply call it whatever you wish, but we now have the thoughts of the executive producer of the series in question on the matter.