The 40k universe is vast and home to many smaller factions that aren’t covered as full fleet lists. Below are smaller collections of vessels for scenarios.
Adeptus Mechanicus: The followers of the Machine God of Mars can draw up a small selection of ships including a Battleship, Cruiser and Light Cruiser. I painted these in the classic Mechanicus black and red scheme.
Grey Knights: The daemon hunters of the Grey Knight Chapter can lend their assistance in the form of a single Strike Cruiser.
Space Station: Painted in the same scheme as my Imperial Fleet, the Space Station makes a great central objective.
Traders & Orbitals: In an age of constant warfare, even civilian craft have to look to their own protection. The selection here includes a Rogue Trader ship, a Victory Class System Monitor and a small Orbital Station.
Cargo: I picked up a few models from a 3D printing shop including three smaller Gazel Class Transports and a large CargoBull Class Transport.