I will preface this by saying that I really don't have that many Doctor ships.
Doctor/Rose - OTP FOREVER. This is *why* I don't have that many Doctor ships, because I just want my Doctor/Rose happy times.
Doctor/TARDIS - Without having seen any of season 6 still (aka, no Doctor's Wife viewing) I still have to admit this is the most constant "relationship" he has.
Doctor/Master - More in a 'I'll buy they have a past and now things are particularly complicated' way. I don't so much ship them as...understand why people do.
(Honorable mention: Doctor/Rose/Jack - not a pairing though, so I didn't list it)
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Doctor/Rose - OTP FOREVER. This is *why* I don't have that many Doctor ships, because I just want my Doctor/Rose happy times.
Doctor/TARDIS - Without having seen any of season 6 still (aka, no Doctor's Wife viewing) I still have to admit this is the most constant "relationship" he has.
Doctor/Master - More in a 'I'll buy they have a past and now things are particularly complicated' way. I don't so much ship them as...understand why people do.
(Honorable mention: Doctor/Rose/Jack - not a pairing though, so I didn't list it)