The DS9 Millenium Trilogy's War of the Prophets
deserves a mention, even if it was undone at the end. The Grigari came along and basically ended the Dominion War (by ending the Alpha Quadrant Dominion), wiped out the Klingons and Earth, destroyed many other worlds and fleets with an insane variety of tactics (from hiding in the mirror universe to using nanites to Red Matter-like singularity bombs)...
Also the devastating alternate-timeline Second Romulan War alluded to in Watching the Clock
(from the unmade animated series Star Trek: Final Frontier
), where much of subspace in the Federation was destroyed by Omega detonations rendering warp drive useless.
There was also Diane Duane's Second Romulan War in The Empty Chair
, in which almost the entire Rihannsu military was wiped out by the Federation and enourmous Rihannsu civilian/colony craft.