Guinan's definitely one I didn't think of - since we know she'd been on Earth before the NX-01, there's no reason why she couldn't have used it to hitch a ride off the planet...
As to the Starfleet one, I have to admit I think the first few eps of TOS shouldn't be counted towards canon - after all, do you really think that the ship should have been equipped with a 'materialiser' instead of a transporter? Or that they should have used the 'old' warp scale?
(Actually, I don't remember them saying one way or another which warp scale they used - tOS or tNG...)
The borg and ferengi eps were both pointless, and its very, very hard to imagine there not being records of the two, and the Enterprise-D crew never noticing the connection. Especially Data or Wesley.
The Xindi war was, as evay said, pointless... and if they needed a war, why not use the Romulan War instead? It could easily provide a season or so of storyline, it would have given a better reason for the unification of Humans, Vulcans, Andorians and Tellarites then the lone raidership did... and I think we can all agree, that if they were planning to violate continuity, then a war and species noone remembers would be far less burdonsome then merely moving the date of a war we know *did* happen.
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