The Clown Prince of Crime
Super Freak
Wolverine remembers everything from the original timeline so technically all movies "happened" with the possible exception of Origins. I didn't catch any glimpses from that one when Logan was having his Stryker flashbacks so it's possible that Singer just ignored it completely.
If you're asking "do X1 and X2 exist in the new timeline" then I would think that based on the last shot of DOFP the answer would be no. Charles makes a speech about how the future is never truly set (indicating that things will not necessarily play out as they did before) and then we see evidence of that with the Stryker/Mystique reveal. For X1 and X2 Stryker was never Mystique (well prior to X2 anyway) so I'd say the butterfly effect would probably have those two movies play out differently than how they went before.
I wonder if those possible changes include Logan's fashion sense As long as he dresses like this in Apocalypse, and HT makes the figure, I will be satisfied.
then again, it's the 80's so he might look like Don Johnson from Miami Vice.