First thought is that flavor wise, having alot of the buildings get small bonuses with mana would be cool. It would also cause people to dirversify mana more(rather than games where I'm not going to be building mages, and I just stack law mana to reduce maintance costs). This would also add a bit more flavor to the different races, since they start with different mana, and thus if a good number of early buildings were modified by this mana, they would all play out at least slightly differently. The other idea would be to make some mana types valuable at the start(for example I never build nature mana before the mid game at the least; as air, fire, body and enchantment are always priorities over things like nature, spirit and shadow magic)
Some ideas: smokehouse + fire mana, better control of the fire, has a higher success rate with preserving the meat, gains an extra 5% food saved on growth.
grainery + nature mana, rodent control via mana, more grain saved, another 5% food saved on growth.
Training yard + law mana, More diciplined training, slight boost to training rate
forge + fire/force/creation/earth. Minor production? boosts for each of these types of mana(2.5% each?) and perhaps drop the production boost of the base unit down by 5%,so its the same with 2 of them,and higher with 3 or 4.
theater + shadow magic, extra happiness or culture due to better plays.
nature mana + animals, rather than building a cage, build a tamed pet that lives in the town(if a panther in a cage is impressive, a panther wandering around town is more impressive), extra culture for each of these.
each of the temples should perhaps get a minor boost with the type of mana that the shrine of that religion produces.
lighthouses and harbors should get a small boost from water and air mana(perhaps trade route or food related?).
market + spirit mana(people with hope are better consumers?
) gains an extra point of money(or perhaps 1 great merchant point a turn)
elder counsel + spirit mana, 1 great sage point a turn; +mind 1 beaker or 5% research boost; + arcane 1 beaker or 1 gs point?, perhaps should start at a single beaker rather than 2 if it gets all of these boosts.
weaponsmith + enchantment mana, minor promotion that increases strength(perhaps 10%?)(on this note, I'd love to have weaponsmith actually give a base promotion(tempered or quality weapons?) along this line as well, the minor military production boost on this building rarely makes it worth building, the only time I ever have these is from the wonder).
library + law/mind mana, better orgainized library helps research, +1 beaker
pagan temple + spirit mana, 1 great priest point
Some ideas: smokehouse + fire mana, better control of the fire, has a higher success rate with preserving the meat, gains an extra 5% food saved on growth.
grainery + nature mana, rodent control via mana, more grain saved, another 5% food saved on growth.
Training yard + law mana, More diciplined training, slight boost to training rate
forge + fire/force/creation/earth. Minor production? boosts for each of these types of mana(2.5% each?) and perhaps drop the production boost of the base unit down by 5%,so its the same with 2 of them,and higher with 3 or 4.
theater + shadow magic, extra happiness or culture due to better plays.
nature mana + animals, rather than building a cage, build a tamed pet that lives in the town(if a panther in a cage is impressive, a panther wandering around town is more impressive), extra culture for each of these.
each of the temples should perhaps get a minor boost with the type of mana that the shrine of that religion produces.
lighthouses and harbors should get a small boost from water and air mana(perhaps trade route or food related?).
market + spirit mana(people with hope are better consumers?

elder counsel + spirit mana, 1 great sage point a turn; +mind 1 beaker or 5% research boost; + arcane 1 beaker or 1 gs point?, perhaps should start at a single beaker rather than 2 if it gets all of these boosts.
weaponsmith + enchantment mana, minor promotion that increases strength(perhaps 10%?)(on this note, I'd love to have weaponsmith actually give a base promotion(tempered or quality weapons?) along this line as well, the minor military production boost on this building rarely makes it worth building, the only time I ever have these is from the wonder).
library + law/mind mana, better orgainized library helps research, +1 beaker
pagan temple + spirit mana, 1 great priest point