All structures that benefit your entire empire (all trade goods, most galactic achievements, stuff like that) ignore bonus tiles.

Some buildings that only affect the planet they are on also ignore bonus tiles. Power plants, research coordination buildings, tech/manu capitols, food distribution centers, etc do not gain anything from bonus tiles. For food, research, and manufacturing production only buildings that give actual output can benefit from bonus tiles. Anything that says +x% toany of those three categories will ignore the tile.

Morale and influence buildings will gain from tiles, unless they are the aforementioned empire-wide buildings. The political capitol can benefit from either morale or influence tiles, as can any building that gives a bonus to both things.