When not playing Creative, do you pick Hydroponic Farms (+2 food on any planet) or Biosphere (+2 population max on any planet) ?

EDIT:
And while I'm at it, for the first Construction pick: do you get Anti-Missile rockets, Reinforced Hull, or Fighter Bays?

Pick Biosphere unless you're short on food.

For Construction, I'd say Reinforced Hull is most useful.

For Hydro vs Bio, early game if you're going to radiation or barren worlds for the minerals, hydroponics will be useful if you don't have enough food. If you do have enough food to support population on radiated/barren worlds, then biospheres will give you more population on each world type.

For construction, it's really reinforced hull vs Fighter bays for me. I tend to go with reinforced hull, but fighter bays can be useful too if you like to build carriers. I know this wasn't in your question but it is related somewhat. Battle pods is a must, especially if you go with fighter bays, but even in general I find battle pods to be the best choice in the pod research field.

Honestly, fighters have always seemed pretty useless to me. A few point defense lasers and they're zapped into oblivion. Reinforced hull, however, is good from start to finish in MOO and can really give you an edge in a fight.

I have never even tried fighter bays. Next game I'll do that, and try very hard to steal (or trade for) Reinforced Hull.

Fighters can be quite useful used right. Fighters are good for taking out light targets (frigates + destroyers) and providing escort against bombers, missiles, other fighters, etc ... A couple of well-placed carriers can use the fighters as essentially a long range point defense force for the entire fleet. Thus when designing your other ships, you can focus more on killing weapons and put fewer point defense weapons on them. Fighters are expensive in terms of space so battle pods for carriers are a must. It's also good (though not necessary if you don't have the space) to have a couple point defense weapons for carriers as when they release all of their fighters they make tasty targets for missiles, bombers, and the like. Even with point defense weapons, keep the carriers rearward after they've released their fighters and only bring them forward to retrieve their fighters so they can put them out again quickly (be careful without fighters, or later bombers, or even later fighter-bombers, carriers cannot engage enemy capitol ships themselves). Also in the design screen keep each fighter group as a separate weapon so you can release them at multiple targets easily and holds some back if you need to.

I tend to research reinforced hull and try to get fighter bays from someone else, but naturally the other way works fine too. :) If you're not used to using fighters in battle, it may require a readjustment of how you design ships/fight, but it can worth it and fun.

Fighters as a defensive technology? Hmm, never tried that. This is worth investigating. Hopefully I'll stand corrected, as it always made me sad that I couldn't find a use for such a sci-fi staple.

Aye they are also better in numbers - en masse they can be quite deadly against even larger ships because even though fighters only have point defense weapons, they get in close and rarely miss. So a ton of fighters on a single target can even make larger targets think twice about an engagement. But that's only if you have a lot of them, fewer numbers and point defense weapons will take them out, though you can use missiles as a distraction - i.e. if you launch missiles from other ships the point defense weapons will have to choose between missiles and fighters - unless they also carry anti-missile rockets, but then if their ships have lots of anti-missile rockets and point defense weapons, your capital ships with more aggressive weaponry should be able to outmatch them since your enemy has spent more of their space on defensive weapons and your killing ships have not. Bombers (depending on how good your bomb tech is) and fighter-bombers can be extremely deadly against any capital target though again in numbers to ensure they reach their targets. Fighter-bombers can also function as escort since they fulfill both roles. Primarily the interceptors are for long range point defense, but can be used against light targets which have less point defense or en masse against any target. Carriers also don't have to be very maneuverable, fast, or well armored since they stay back from the fight, so you can fill them to the brim with strike craft. If the carriers get in a tight spot and they've launched their fighters, simply retreat them - the fighters stick around until their weapons are exhausted.