I think there are some possibilities. For example, what if they found Data's head before the TNG characters did from [name of episode here] and discovered to save history they had to replace the head in exactly the same location they found it while the TCW baddies (I still think that should've been the Romulans) were trying to find it and dig it up. What if they entered the space in Tholian Web (TOS) and saw Kirk suspended in time, interacting with him. (Impossible with Shatner being so old, but it could provide for some interesting character development for Archer.)
I think whatever episode they chose, it shouldn't have involved the Borg or Q. And I think the hard part is it might be best, despite the suggestion above, for them to stray from time travel episodes. One of the things that ENT did that became cumbersome was using time travel as a fix.