Setup waypoints and have the shipyard send ships to that point.

I just rally point to itself and launch manually.  Problem is, I keep forgetting the ship is there.

There was a little button in the command window for the planet that would let you set it manually (I never knew about a hot key).  (There are no shipyards in GC2.)

I still haven't figured out how to set a rally point from a shipyard.  Clues?

Ok for me (Crusade) on minimap (lower right corner of map screen) it has four(4) tabs above it(beehive, graph, hand, Rallypoint). 

1. Click on rally point tab
2. Click "New" button which changes the cursor 
3. Click anywhere on main map and it will create a new rally point.
4. Then select shipyard and click "Rally point" and select your new rally point from the list.

Note: I believe this only works for new ships and does not seem to work for ships which are ejected from shipyard.