Rogue Trader
The forces of a powerful Rogue Trader can be a fleet in and of itself. While Rogue Trader vessels are available, and entire fleet based off the Imperial Fleet can be made. The Rogue Trader Cruiser, Escorts and Monitor ships are the most obvious components, while additional Imperial ships, such as light cruisers, frigates, escorts and fighters, could reasonably have come under the control of a Rogue Trader. Mercenary forces from Ork or Kroot might also be utilized, probably under counts-as rules.
Adeptus Mechanicus
Adeptus Mechanicus ships are also available as part of a standard Imperial fleet but could also be expanded into a fleet of their own. Mechanicus Explorator fleets are dispatched across the galaxy and could form the basis for a tabletop fleet. Any Imperial ship could be used, with suitable modeling and painting, such as Mechanicus cog icons and red and black paint schemes. Ancient or alien technology can be represented by using parts from practically any other alien ship miniature.
Pirates
Though Eldar corsairs are the most famous, human pirates do exist in the Warhammer 40K universe. Jury-rigged pirate vessels made from various components of Imperial ships are a modeling challenge that can result in a distinctive fleet on the tabletop. Such a fleet can also include scavenged ships from other races, sometimes in a haphazard fashion.