When you say cliffhanger I assume you are referring to the actual ending as opposed to the best cliffhanger episode as a whole so my favorites:
The Best of Both Worlds Part I--best cliffhanger in Trek or tv period.
Call to Arms--the Federation is at war finally, Jake is on the station, Kira/Quark/Odo stays behind, Dukat back in charge of DS9 with sights set on Bajor, the awe-inspiring sight of the Defiant and Rotarran joining the massive fleet as screen goes to black.
Redemption I--Sela stepping out of the shadows
Descent I==Picard/Troi/Geordi surrounded by menacing Borg and Lore's "The sons of Soong have joined together and together we will destroy the Federation"
Unification I-Spock at the very end
In Purgatory's Shadow-with the fleet of Dominion ships pouring out of the wormhole
All the Final Chapter episodes had strong final scenes--Sisko/Sarah, Section 31 responsible for the virus, Damar's resistance, the cloning facilities destroyed, the Breen joining the Dominion.
Azati Prime with the brutal assault on the NX.
The Council with the launching of the weapon and Hoshi abducted.
Zero Hour with the Alien Nazis which I liked.
Scorpion I with VOY in tow following destruction of an entire Borg planet.
Unimatrix Zero with Janeway, Torres and Tuvok as Borg. Not as powerful as the sight of Locutus but still impressive.
Broken Link--"You're too late we're everywhere"
The Jem'Hadar-"If the Dominion comes through the wormhole, the first battle will be fought here. I intend to be ready for it."
I alo enjoyed in "Kir'Shara" where the screen goes to black then fading into a clandestine meeting between V'Las and a Romulan. It was ominous as the Romulan spoke of plans of unification.
I also loved the clever reveal of Valdore actually being on Romulus as the camera panned outward from one of the capital city's spires. United had the intriguing reveal of the albino Andorian seemingly working with the Romulans.
Those are the ones that stand out for me.
