Technically speaking, X-Men Origins: Wolverine comes first in the order, since it begins with Logan (née James Howlett) as a child in 1845. But it quickly jumps forward in time to trace his relationship with his half-brother Victor Creed through many decades and multiple wars, ultimately settling in around the late '70s/early '80s for the bulk of its plot, between the events of Days of Future Past and Apocalypse. So for the purposes of this timeline, we're going to put it third, because putting it first would be both confusing and misleading.
However, while the first century-plus of Logan's life remains untouched, it's hard to know for sure whether all of the events that take place during Wolverine still actually even happened, due to the timey-wimey shenanigans in Days of Future Past. When future-Wolverine helped reset the timeline, he may have altered several events from his own past/future. He definitely still received his adamantium skeleton, which implies that most of his encounters with William Stryker still occurred (which later seems to be confirmed in X-Men: Apocalypse), but as for everything else that transpired during Wolverine — including the creation of an uncharacteristically mute Deadpool — it may never have occurred at all.