I very rarely max out resources. However, when I do, I do thing similar to what the others in this thread have said:
- Zenith Trader projects
- Extra turrets/mines
- Capital Ships
Mercs are always the default fallback, because they will eat through any resource surplus with no problem, and the ship caps are so ludicrously high that you'll never reach them before you have to shut down the merc dock and build something else.