Black Prophecy is probably already on your radar screen. If you're looking for a space-based MMO that has a bit of crafting complexity, take a second look at the upcoming free-to-play MMO from Reakktor and Gamigo.
In addition to modular ship-building, Black Prophecy also features a traditional crafting system for ship and station components. The game boasts three resource types: metal, plasma, and gas. Metals, as you'd expect, make up modules and weapons, whereas plasma serves as the crafter's source of power. Gas is required for high-performance computer production and for the ubiquitous hyperspace drives. All three resources can be salvaged from space junk as well as procured from successful missions.
How do you put all these parts together to construct the ultimate interstellar interceptor? With blueprints of course, which are found in the wreckage of old starships. Once blueprints have produced a module, they can't be reused. If crafting fails, however, you get to keep the blueprint (but not the resources) and try again. Finally, Black Prophecy's crafting system will feature optional items called constructors. These units are used during the crafting process to enhance success chances or shorten construction time, and may be modified or repaired by players.