All of those had weaknesses
1. The Borg were defeated,
2. The Replicators where held indefinitely in a statis field.
Now the Q - beings that were only (as I recall) weak against their own kinds - now THEY could be definite contenders.
That's cheating... the Q were pretty much godlike.

What about the aliens from the thirdspace in Babylon 5? They were even stronger than the first ones (vorlon, shadows, etc).