Weapon Speed / Armor Health -- Pick you favorite. I prefer Weapon Speed, as it becomes the better option once you consider SCVs / Medics / Science Vessels
Orbital Depots / Micro-Filtering -- if you're good about supply management, go with micro-filtering. This one is also a toss up.
Automated Refinery / Command Center Reactor -- depends on your macro ability. The Reactor becomes slightly more valuable on higher difficulties, but the Refinery enables long-distance vespene harvesting.
Raven / Science Vessel -- Pick Science Vessel for machine repair, unless you really like Ravens.
Tech Reactor / Tech Reactor -- No contest.
Shrike Turret / Fortified Bunker -- Fortified Bunker. The turret is basically equal to a single marine. Fortified Bunker gives it the health of +6 marines.
Planetary Fortress / Flame Turret -- depends on playstyle. Some folks like to spam planetary fortresses on the defense missions, others appreciate the flameturrets. Another tossup.
Predator / Hercules -- neither unit will see much use, firebats / hellions easily outstrip predators, and there is very little reason for drop play in the campaign. That said, the Hercules is very helpful on certain missions, such as the Moebius Rescue mission (exact name escapes me)
Regeneration / Bonus Energy -- The regeneration is very slow. Besides, you have SCVs / science vessels! +100 energy = longer cloaking, more yamato cannons(!), more psionic lash(!), and more healing for medic / science vessel. If you use Wraiths, Banshees, BCs, Ghosts/Spectres, Medics and/or SVs, go for the energy. The regeneration is quite slow.
Hive Emulator / Psi Disruptor -- Depends on playstyle. Emulator requires more micro. Both are helpful.
You can find some additional discussion here.
Edit: Were you looking for armory purchase suggestions as well?