RTD has said on more than one occasion that Genesis Of The Daleks - where the Time Lords send the Doctor to alter or avert the Daleks' development, and in the process inadvertently bring themselves to the attention of Davros and the Daleks - is the first volley of the Time War.
Just for fun, where else might we have seen the Time War taking place without even realizing it?
My early picks:
The Space Museum / The Chase: the Daleks are stalking the Doctor through time with their own time technology, trying to eliminate him before he can thwart any more of their plans. Given that this is the first time we see the Daleks with their "solar power slats" - which they'd have for the remainder of the classic series - these could be Daleks from the far future, trying to eliminate the Doctor before he really starts interfering with them.
Resurrection Of The Daleks: the Daleks are planning to clone the Doctor and send him to eliminate the High Council. This scheme is wacky and convoluted enough to have "Cult of Skaro" (or "Eric Saward") written all over it.
Remembrance Of The Daleks: Davros happily declares his intention to do away with Gallifrey and the Time Lords. Not just another day at the office.
Honorable, but blazingly obvious, mention: Big Finish's The Apocalypse Element: well duh! Daleks invading Gallifrey! Does it get better - or more obvious - than this? Clearly the Time War is in full swing - and the sixth Doctor's in the middle of it. This raises the question of whether or not the Time War was in progress for many/most of the Doctor's incarnations as a - and I shudder to use this Enterprise-ism - "temporal cold war" before suddenly heating up into open warfare during the eighth Doctor's time.
Any other obvious signs of the Doctor being screwed with from his own future? They don't even have to be Dalek episodes.
