"Weapons Upgrades grant 5% increased attack speed" or "Armor Upgrades grant 5% more HP"
This is a tricky one -- but ultimately, it really comes down to unit comp.
Ask yourself -- do you intend to invest in medic / repair tech? The longer any individual unit survives, the more it benefits from increased attack speed. Raw health only matters in the absence of SCVs, Medics, or Science Vessels. If you buy the bunker upgrades -- it makes sense to go with the weapon upgrades -- units can't benefit from increased health when they're in the bunker after all.
If a marine usually has an attack speed of .83 seconds / attack, and the weapon upgrade reduces that by 5% ( to .78 ), it takes 5 attacks for the marine to benefit from the extra attack speed (both make 4 attacks in 3 seconds, but after 4 seconds, the upgraded marine has made 5 attacks, and the unupgraded marine has made only 4 (but is about to make a fifth)
The longer you can make your units survive, the greater the benefit.
Bonus health doesn't make sense on the weak, individual units who will die quickly anyway.
It, on the other hand, works better for stronger, more expensive units who are already taking several hits to down. A battlecruiser's 400 hp goes up to 420 -- which means it will survive two attacks more from a mutalisk swarm (discounting armor)
A marine would only go from 45 HP to 47.
Because of all of that, I think it's better to go with weapons speed than bonus health.