I created a custom race and loaded up a series of test games with it. In each case I made sure the race's bonuses were only from 1 of each of the 4 categories, Research, Economic, Social, and Military (as well as once with no bonuses). I then modified my taxes and spending to try to isolate the effect of each bonus. This is what I found:
Bonuses to Military and Social production were applied to colony production exactly as given, +50% = +50% Effective production BASE... For example, on a starting planet if you had +50% Military your base production for calculating Military spending would be 36 (24*1.5). So with maxed spending, and production evenly split between Military, Social, and Research you would spend 12/8/8, as expected (8/8/8 is normal on starting colony, so 8*1.5=12/8/8).
The upside is that you get a lot more production from initial colonies and all factories. The downside is that you still have to pay BC for every single point of production gained, thus raising your expenses considerably.... You gain the potential to build much faster, but at the cost of needing a lot more BC to fuel your production.
With Research bonuses I found something completely different. You would expect Research to be the same as above, however, what I really found was that a Research bonus doesn't increase your research base, or expenses, at ALL. Instead HALF the bonus is applied to your research AFTER you pay for it.... So if you have a 50% research bonus, max your spending, and split it evenly between Military, Social, and Research, then instead of getting expenses of 8/8/12 your expenses will be the normal 8/8/8. However, on the planetary screen your research number will show 10 research, a 25% increase, which is exactly half the bonus you would expect, but also a BC FREE bonus.
Economic bonuses add exactly the percentage given (less rounding) to your tax income BEFORE bonuses from planetary improvements, like Markets, are added (and presumably before economic starbases as well). This makes Economic bonuses incredibly valuable as they are multiplied by further bonuses instead of added.
Morale also provides a bonus, the exact details of which I did not investigate, but in general it seems decent, but not great. However, it is still nice because it allows you to have a higher total population, or charge higher taxes, or both, which ultimately increases available BC, which leads me to my main point...
The reason I think the information above makes Economic, Research, Morale bonuses superior to Military and Social bonuses is because there is only 1real resource in the game... BC's, and these bonuses directly, or indirectly provide you with MORE BC's while the other two just free up a planetary tile or two. Admittedly those free tiles could be used to increase BC's, but not as effectively or efficiently as these bonuses do....
If you aren't at or near 100% Industrial Capacity then you are effectively wasting a lot of planetary tiles. Past a certain point all increasing planetary production and research tiles really does is focus more production on that specific planet.
I am not suggesting a cookie cutter approach to min/maxing custom races, especially since the BC savings/income from Research and Morale aren't nearly as great as from Economics. I am just trying to spread some useful information that isn't immediately obvious to most people, and yet which is vitally important to understanding the game and playing effectively.