With the economic unlocks, I tend to wait until I've got 5 economic command stations before unlocking the MkII economic station, and wait until I've a further 5 before locking the MkIII. This maximizes the resource income benefit from spending the knowledge. Then I shuffle things around so that the MkIII stations are on the closer in worlds and less likely to get destroyed. At this point I start to think about upgrading the harvesters, upgrading whichever resource has the lowest income, as by this point there should be a fair few harvesters built and again the benefit of spending the knowledge is maximized.
As mentioned before, grav and tractor turrets are great for buying time, as are riot starships (I usually stick to lasers on them for maximum range, keeps them out of trouble) for their engine damage abilities. I'll often mix light starships in with my missile frigates to give them the damage boost and provide some short-range defense in case anything gets through.
Not spending knowledge until you need to is also very good advice. I'll often wait for a difficult looking wave to be announced before unlocking a ship or turret (or both) to counter it.
We're talking Dwarf Fortress fun, right?
What other kind of fun is there!
Well, this may be controversial, but I sometimes find winning fun too