Well we know he saw some pretty bad things (I mean its been heavily implied that he's the one who created the 'Burning' that destroyed the Time
Lord and Dalek races).
And let's not forget the end of Family. We were told he killed out of kindness and the Family (who REALLY made him mad) each suffered fates worse
than death.
I don't think the Doctor is squeaky clean at all. War changes people.
EDIT: Oh yeah, RTD confirmed that the Time War was due, in part, to the Time Lords sending the Doctor back to prevent or alter the creation of the
Daleks. Presumably the Daleks found out and, being Daleks, mounted their own offensive. My guess is they then tried the same tactic on the Time
Lords.
Its interesting to note that one of the Time Wars involved the Time Lords fighting various races who were developing time travel and one of these
enemies was destroyed before it even existed!
Time travel is confusing
[edit on 4/6/07 by JackofBlades]