The GunStar from The Last Starfighter blew me away as a kid. Pretty good CG for the era as well, but the design felt sleek and believable.
I've always loved the Vipers from BattleStar Galactica as well as the Veritech from Macross (well... robotech since that's what it was called here when I was a kid lol) but I feel like those are both pretty mainstream now?
The morphing ship from Flight of the Navigator was pretty cool. In that same era, the bubble ship from Explorers was pretty awesome concept.
Do personal vehicles count? I always wanted to have a Light Cycle from tron. I loved that they just turned it on and their disk became the steering and it just formed around them. Plus it was cool af. The Cylcone from Macross / Robotech was pretty cool in that same vein.