Board Thread:The Reference Desk/@comment-60605-20140919101627/@comment-1827503-20140926185603

The First and Fifth Doctors' eras narratively link each story to the next, but we have no such recourse for the Second, Third, Fourth, Sixth, or Seventh. We assume the Doctor's timeline is in broadcast order for classic Doctor Who because there is rarely evidence to the contrary.

BBC Wales Doctor Who generally makes an effort to definitively place the stories in broadcast order from the Doctor's perspective, except for occasional hiccups like A Town Called Mercy. The spinoffs, on the other hand, got screwed up by DW not airing a full series in 2009, which caused a dating problem similar to the UNIT problem in the classic series.

tl;dr: The Doctor's timeline within televised Doctor Who is generally in broadcast order, but the BBC Wales-era spinoffs may not be in broadcast order.