"A Time to Kill" and "A Time to Heal" have battles of all shapes and sizes aplenty along with a compelling plot with implications that continue through several other books. There's also "Destiny", which spans time, space, and most of the series.
"Vendetta" also has a big Borg battle with the crew trying to rehabilitate a former Borg drone(something like the Seven Of Nine arc, but better). Then there's also "Capture The Flag". Giant War Game training story involving Geordi LaForge at the Academy.
I don't know if it fits your definition of "large scale" or not, but "The Wounded Sky" has an excellent battle scene between the Enterprise and a squadron of Klingons, at least 7 or 8 ships if memory serves. The Klingons do all of the actual shooting but (spoiler alert) the Big E comes out on top.
IKS Gorkon: Honor Bound has a pretty big battle between about a dozen Klingon ships and tons of ground troops. The MU stories like The Worst of Both Worlds in the Glass Empires omnibus and Rise Like Lions had some pretty big battles as well.
I think there's a pretty big ground battle with the Voyager crew and some Klingons in Full Circle, the first book in the current Voyager Relaunch series.
How about "The Return" by William Shatner? Another good Borg story (with the Romulans) that could've been the theatrical sequel to "Generations".
Typhon Pact: Rough Beasts of Empire opens with pretty epic battle, concurrent to Destiny. The rest of the novel is space-battle-free IIRC. Voyager: Children of the Storm has some chaotic fighting. Before Dishonor features some insanely outrageous fighting between a Borg super cube, a planet killer (it's actually a sequel of sorts to Vendetta) and the Enterprise-E. There's also a mutiny and... someone dies. That was a cool battle, but it should be pointed out that it's very different from the battles in TV/film Trek, and how some technology works and the effects of warp drive around stars is totally different to what is generally currently accepted.
DS9: The Soul Key has a lot of battles, including a ground attack on a Bajoran settlement by the Klingons.
Rise like Lions has some pretty nasty large scale battles, but it's placed in MU. Other than that, The Romulan War: To Brave the Storm has some very good battle, at the end.
"Ragnarok" has a pretty big, and old, battle. Plus "Battle Lines" (Voyager#18) has the Voyager and crew drafted into an alien war, with everyone, except Janeway, as I recall, assigned to different alien ships. "Cathedral" also features a major battle. But with Shatner, he also co-wrote a Mirror Universe Trilogy that is probably the best Mirror Universe story out of all the MU stories. But how would you like to see the Klingon/Cardassion Alliance try to take over the Federation with the help of Kirk's doppelgänger, Tiberius Kirk?