Been having fun working on parts of the base for my current freighter. In the process of which I accidentally found out that if you place a piece of the legacy freighter base parts in one of their specific colours, and then place new freighter base parts without accessing the colour selection menu, they'll will show up in the colours of the legacy part. Which means I suddenly have a lot more options for base building colours.
The ground floor of my base has (facing aft) a small room on the right with the system scanner, teleport, and construction supervisor's desk. Across the hall from it (on the left) is a large room with all the storage units, a refiner, three orbital collectors, exocraft materializer, and exocraft technician's station. At the aft is a room containing a galactic trade room and five fleet command stations.
Upstairs from all that I've done my usual spacious greenhouses; there's two 5x5 rooms where I grow the majority of the plants, a 7x4 room (less 4 tiles for decor) where I have copious amounts of frostwort for glass making, and a 3x5 room of nipnip for profit. Adjacent to the greenhouses is the agricultural specialist's workstation and a little food service/lounge area, plus some exterior platforms.
Still need to work on areas relevant to the weapon's technician and scientist; that'll probably be placed on the first level to either side of the fleet area.