The X-wing (Star Wars): a classic. In the EU, it's shown that they have multi-directional particle and ray shielding, hyperdrives that can take them across a decent fraction of the galaxy in mere hours, projectile weapons that detonate with the force of small nuclear weapons, and can spin on a dime with competent pilots that can manipulate their engines and thrusters correctly. Oh yeah, and four cannons in the cool combat formation thingie. Plus, you can have you astromech droid along for the ride! That, or stuff a spare one in the cargo hold they all come with. Also, ejector seats in case things go south. Gotta love the X-wing.
The Shadow Battlecruiser (Babylon 5): a living ship that, despite not having your sci-fi standard shields, is among the most ridiculously resilient things in that entire series. The bio-technology used to created them means they self-repair, never run out of energy, and absorb the vast majority of all energy weapon discharges that hit them. They use living humanoids permanently trapped at their core as a CPU (scary ass fate), make a scream in your mind as they pass by, and look like Death itself mutated into a giant space spider that's black as the deepest night. They can drop in and out of hyperspace at a moments notice without creating the standard jump gate most species need AND have the ability to collapse such gates, destroying any ships momentarily caught in them. It's primary armament is a beam weapon whose power output is strong enough to cut straight through and destroy virtually any other ship in the show and they never miss unless they intend to. Last but not least, each one can launch dozens of autonomous fighters of its own to swarm the enemy and keep their fighters busy. They are utterly terrifying opponents in a fleet combat and worth every drop of the terror they inspire.
And my personal favorite...
Tengen Toppa Gurren Lagann (Gurren Lagann): a ship that is also mech with is actually several mechs each inside each other that is fueld by sheer willpower strong enough to warp reality on an utterly insane level. Simon and team Dai Gurren used it to go into an artificial parallel universe and fight the god-like beings known as the Anti-Spirals, whose stated goal is the subjugation and/or annihilation of all other sentient beings in the universe. When fully powered up, TTGL is the size of an entire galaxy and can use attacks powerful enough to shatter worlds and stars by the hundreds in a heartbeat. It also has the best damned battle cry ever, "Who the hell do you think we are!?" One of the most ridiculous and badass ships in existence from one of my top 3 favorite anime.