After watching Star trek Into Darkness I have fallen In love with the USS Vengeance. I love that ship, but Star Trek has more than just one awesome bad guy Starship, so in this list I will be talking about my personal favorites. Enjoy.
Built in secret in orbit around Jupiter the Dreadnought-Class USS Vengeance was the Flagship of Admiral Marcus and section 31. In 2259 (Alternate Reality) the Vengeance pursued the Enterprise to Earth where a battle (more like one sided slaughter) occurred between them.
While the Dreadnought-Class has been mentioned, it has never been seen on screen in the Prime Universe. So not much is known about that one. In the Alternate reality The Dreadnought-Class is twice the size, Twice the firepower and three times the speed of an alternate Reality Constitution Class starship. Designed primarily for military purposes this ship could pursue and catch up to another ship at warp, and could also fire its weapons at warp, without destabilizing its warp field.
The Vengeance was a beast, designed to mostly automated the ship could run with a minimal or even one person if needed. It was destroyed when it crashed into San Francisco.
The USS Lakota was an Excelsior Class refit in the 24th Century. Commanded by Captain Erika Benteen. in 2372 the Lakota was ordered by Admiral Leyton to intercept the USS Defiant and disable it to prevent it from reaching earth.
At the time Admiral Leyton was attempting a Coup d'état of earth because he felt that the Federation president didn't take the threat of the Changelings serious enough, so he decided to take matters into his own hands. At the time the Defiant was ferrying a witness to earth to testify against the admiral so he had the Lakota intercept the ship.
What the defiant crew didn't know was that although the Excelsior class was an old ship The Lakota was upgraded with Advanced shields, phasers and carried Quantum Torpedoes on board. The fight was short but eventually The Lakota stood down when Captain Benteen was ordered to destroy the Defiant.
The Romulan drone ship was a modified 22nd Century Romulan Bird of Prey. in 2154 due to increased partnership and Corporations between the Alpha Quadrant Powers (Starfleet, The Vulcans, The Andorians and The Tellarites) the Romulans sought to destabilize the region. Its easier to conquer a region if the people living there are fighting amongst themselves.
This is where the Drone Ship Comes in; coated in Multispectral emitters, the drone ship could create a holographic replica of any ship it wanted. Armed with Triphasic Disrupters the ship could replicate the weapons signature of of any ship it wanted. Even though the Andorians and Tellarites were on the road to peace, things between them were still very rocky. So when the Romulan Drone ship (disguised as a Tellarite cruiser) attacked and destroyed an Andorian Cruiser tensions between them were high. Luckily the crew of the Enterprise figured out what was going on.
In addition to the its shield and powerful weapons another advantage the drone ship had over other ships was the fact that it was remote controlled. The ship had no crew on board and was remotely piloted from Romulus. This allowed the ship to be highly maneuverable and quick. Luckily BOTH drone ships were eventually destroyed.
In the 23rd Century both Klingon and the Romulan ships main defence were there cloaking abilities. While these cloaks were not perfect they did make fighting these ships more difficult. The good thing about these cloaks was that they used alot of energy, so if a cloaked ship wanted to fire its weapons it would first have to de-cloak fire then re-cloak again. Due to the cloaks large power needs cloaked ships also would not have their shields up.
Changs bird of Prey did not have this problem though. After framing the Enterprise for firing on Chancellor Gorkon's ship Chang took his ship to Camp Khitomer to stop The Enterprise crew from getting to the peace summit. The Bird of Prey inflicted terrible damage on the Enterprise but was eventually defeated by specialised photon torpedo.
Built by the Remans the Scimitar and commanded by Shinzon the Scimitar was a massive ship. It was built to fight carried numerous Scorpion Class attack fighters on board, making this one of the few if not the first Battle Carrier seen in Star Trek.
A technological Masterpiece The Scimitar could Both go to warp and Fire While cloaked, unlike Changs Bird of Prey almost a century it could do all those things and have its shields up at the same time. This ship was chore to fight and could easily match a Sovereign Class vessel and two Valdore Type ships in a prolonged fight and still be capable of fighting. Its weapons systems were just as impressive as its feature boasting 52 Disruptor cannons, 27 torpedo launchers Primary and secondary shielding and the Crown Jewel A thalaron Biogenic pulse weapon.
The Scimitar was only defeated due Picard desperate maneuver of ramming the Enterprise into it and Datas selfless act.
In 2374 the Crew of Voyager come across an Alien named Arturis with the ability to decode messages. They ask him to decode a highly degraded message from starfleet, once he does they figure out that the message is actually a set of coordinates to a ship. An experimental starfleet vessel named the USS Dauntless. The ship features a new type of propulsion system called a Quantum Slipstream Drive. The Quantum Slipstream drive is more advanced than Warp covering 15 light years in only a few minutes, the same trip would take Voyager two days to cover at high warp.
Eventually its discovered that the ship is just an elaborate trap set by Arturis to take revenge on the Voyager crew for their intervention in the borg Species 8472 war. He believes that if the Voyager crew had just let Species 8472 destroy the Borg then his world never would have been assimilated. His plan is foiled and in a twist of fate the plan he had concocted for the Voyager crew happened to him instead.
By the 26th Century Starfleet adopted the Dauntless design and one was seen at the battle of Procyon V.
Before going back in time 150 years and creating an Alternate timeline the narada Started out as a Romulan mining vessel. Captain Nero had the misfortune of watching as his planet was consumed by a supernova. Long Story short Nero took his ship to the Talshiar (The Romulan Secret Service) who at the time were experimenting with salvaged reverse engineered technology and used them to upgrade Nero's ship. Not only did the ship grow in size but its weapons and warps systems both got a major overhaul due to the borg technology.
From here on out you know the story, the Nero went to meet Spock and both got pulled into the Black Hole appearing in the past. In addition to being able to repair itself (Like borg ships do) the Narada had a very advanced torpedo system, when fired a torpedo would break up into smaller parts and impact a ship at various points. While they couldn't fire through a ships shields they could cause enough damaged to knock them out (and warp drive) in one hit.
The Naradas torpedoes could also fire normally with out breaking up as seen when it attacked the enterprise above Vulcan. Even without breaking up the hit from the torpedo dropped the Enterprises shields down to 32% with the first hit. The Naradas other "weapon" was its drilling rig. Since the the ship was originally a mining vessel it possessed a plasma drill for boring into planets and asteroids. When used in conjunction with Red Matter they could create Black holes to consume planets. When the drill is active it disrupts all subspace communication and transporter signals in the area.
At the Start of the Dominion War Jem'hadar fighters were the scourge of Starfleet Vessels. While federation Danube Class runabouts were more maneuverable Jem'hadar fighters out matched them in Firepower sturdiness. While relatively easy to destroy on their own these fighter possessed a terrible weapon. Phased Polaron Beams, At the time only Klingon Shields could withstand them, but Federation shields were useless against them as they had the ability to fire through the shields and hit the ship directly.
Even a ship as powerful as a Galaxy Class starship with shields at full strength were not immune to these weapons. For a time the only ship capable of standing up to the fighters was the USS Defiant, and that was due to the ships Ablative hull armour. Eventually by the Second battle of Deep Space 9 Starfleet had equipped its ships with advanced shields capable of withstanding Phased Polaron Beam fire.
Like Jem'Hader Fighters Son'a Battlecruisers might lied in their weaponry. While equipped with traditional weapons (photon torpedos, phasers etc) the Son'a Battle Cruisers main weapon of choice was their Isolytic or Subspace weapons. These unpredictable weapons were capable of creating subspace tears which are in turn attracted to a vessels Warp core, and would continue to open until sealed. Areas of space damaged by subspace tears are dangerous to both ships and planets.
Unlike most ships of the time Son'a Battlecruisers were modified to traverse an area of space known as the Briar patch. In this part of space federation ships had to slow to three quarter impulse to avoid clogging and over heating their impulse manifold due to the areas dense gas formations.
In Star Trek Insurrection Two of these Ships chased the Enterprise-E into the briar patch. One was destroyed thanks to some quick thinking by acting Captain Riker.