javaslinger =>
You don't say how early/late your game is, or what your empire's specialties are. Hence, some general notes...
* Trade is one source of resources; so is theft. A single 'bribe transports' (IIRC) operation can take 10k of each resource.
* Certain ships are so obsolete or unnecessary they should/could be scrapped. Old beam ships, for instance, may not have the range or speed to do any damage.
Incidentally, you could also consider moving ships to be scrapped to a neutral system, and then offering them to an AI for a trade (or even a gift, if you really are looking for friends and aren't Mega-Evil).
* Certain ships and bases should be refitted/whittled-down or mothballed. For instance, if memory serves, a base w/ an SY III is more cost-efficient than a base w/ an SY I, so you may be able to replace a stack of SY I bases with a smaller, cheaper, but faster stack of SY III bases. If you don't need them at all for now (and it sounds like you probably don't, since you have so many ships), mothball 'em.
Old missile ships can be mothballed for use as a second-tier defense if the prospect of invasion worries you; missiles work better in numbers, and they'll absorb some PD fire.
Pop transports that had been useful earlier may be mothballed or scrapped.
* Ask yourself whether you need so many ships, or whether you can make do with *few* high-tech ships. For instance, if you have a range advantage (solar collectors or QR), plus a speed advantage (say, solar sail), you may be able to send a number of ships solo (dispersed to hit more targets at once) past enemy fleets (ignore them...) and systematically wipe out all enemy colonies in order of proximity to you. Planet-killing designs can be fairly simple; they only need some shields/armor (to absorb perhaps an attack or two from WPs/sats), a few PDCs, max engines + solar sail, and some planetary napalm (which does *huge* damage). Cloaking and other foo is nice, but optional.
If they can't reach you with any supply left, they'll be sitting ducks even if they *do* come, and they probably won't. Once you start clobbering them, they may not be able to pull their ships back (for scrapping/mothballing) in time to be able to build new ones (due to *their* maintenance cost hampering them). You really don't need that many ships to pull this off, as long as they're good ones.
* To really, really optimize production is best done in a larger quadrant (more time before the fur starts flying), and generally needs:
0 - All three colonization techs. Use every planet...
1 - Planet Utilization tech.
Atmosphere converters, to be more space-efficient.
Value improvement plants -- +3% per year, *each*.
Climate control facilities -- influences population birth rate, indirectly. More people, more production and more potential colonizers.
2. Stellar Manipulation.
For the Monolith III's, and for the planet-makers. Also, I'd recommend wiping out nebulas in your space to make it harder for AIs to hide, just as a matter of principle; and creating stars in empty systems, to help your solar-powered ships.
When you're out of nice planets, make some more.
3. Chemistry / Resource ConVersion.
Combined with M3s, they give you *really* flexible production.
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-- The thing that goes bump in the night