A black market for buying and selling well trained spies. The Mercenaries Guild can sell any spies from any planet in your empire as long as they are on the same planet where the Mercenanries Guild is located.
The Subspace Transporter is a replacement for the Trade Ministry. It allows you to transport items between planets instantly. Its down side is that it requires essentia to pull off that feat.
The Trade Ministry allows access to the interstellar market. Through it you can set up trades for resources, glyphs, plans, ships, and prisoners with other empires. It also allows for pushing resources, glyphs, plans, ships, and prisoners between your own colonies. The newest features also allow for the automated pushing of resources to other bodies via the Supply Chain, and the removal of waste using the Waste Chain. The effectiveness of each of these chains is reduced if the efficiency of the Trade Ministry is reduced.