I have a pretty cool ship (which can also have variable "heads" applied to other series):
Behold, the Deathmask. Named for the signature faceplate that protects the main body and lateral balance engines of the ship. Mostly a front-end blockade runner/weapon of fear/intimidation.
Obviously, the 3-D model isn't complete, but just to give you an idea of what it would look like. It's more airship than spaceship, although with the engine nacelles in the right places, it'll work well in space as well.
Some of the fuselage design was actually inspired by the Khor-Ah Marauder chassis from Starcon 2.
This ship is surprisingly effective; especially in groups of 3+.
Oh, and so it isn't entirely an Achille's Heel, the faceplate is actually bifurcated (and significantly stronger (at least 4x default HP each faceplate piece (2/side)), so there's still plenty of protection, even if one half is gone or too severely damaged. They can also be dismounted/jettisoned as well, and essentially still be a flying repeater cannon.
The true Achille's Heel of the ship is when it's in air and not space, and you knock out one or two of the engines (depending on which ones, and remaining power output set to them); alternative weak points are also the support bars that hold up the mask and the engine blocks (a good solid explosive hit can KO them quickly, and dismantle the target part. Have fun hitting them though. If there's one thing these ships can do well, it's spin (hard to do in-game though. Haven't fixed it yet.)). However, the solid shield and the thrust vectoring system that augments the maneuverability of the craft (so it's always looking at it's target) is a way to protect itself. However, working in teams of 3 or 5 minimize the chances overall of having it's body visible from any other angle. All you see is it's face.
A bit of mythology to place on the chassis, these 'masks' inspire indigenous people to wear such things to "give them strength", as the eyes, nose, and mouth of these faces of doom spouted fire, in which what it sees ceases to exist. Just to give an idea of just how fearsome these things can get, they could be regarded by primitive cultures as "the faces of angry gods".