So far I've seen this to be the best viewing order:

  • Season 1 of Doctor Who
  • Season 2 of Doctor Who
  • Season 3 of Doctor Who, stopping after Blink
  • Season 1 of Torchwood
  • Season 3 of Doctor Who, restarting at Utopia
  • Season 2 of Torchwood
  • Season 4 of Doctor Who
  • Season 3 of Torchwood (Children of Earth)
  • Doctor Who Specials (four hour long episodes in 2009)
  • Seasons 5 and 6 of Doctor Who
  • Season 4 of Torchwood
Although the last two seem to be interchangeable as there are no crossovers at that point.