-Build miniatures at as large a scale as you can afford. 

 -Limit the length of time audiences see miniature effects in the finished edit. 
-Light them realistically, usually with natural light. 
-Mix the miniature effects with other techniques like CG and live-action to confuse the scale and keep the audience guessing. If a person walks through a miniature scene, it's harder for the audience to realize it's just a miniature effect - and with modern compositing, this sort of scale confusion isn't so hard to pull off! 
-Record at high speed, using the square root rule (slow a shot down by half and it seems 4 times as large, slow it to one third speed and it looks 9 times larger, etc. This is with regard to physics of falling or breaking pieces of a model; small things that fall off small models hit the ground faster than big ones off big objects, so you need to slow the motion of the miniatures down to compensate.) 
-Make the model highly detailed and realistic-looking. (My burning dollhouse in Troop 4 TV failed at this, it looked fake so burning it at 60 fps from a believable low angle was insufficient to sell it as real) 
-Structure it like the real thing so if it breaks apart it does so in the right way. (My Duel 2030 exploding bunker at 1/8 scale, for example, looked good but could've been even better if the walls were prescored and a lot of little bricks broke off realistically when it blew up.) 
A bonus tip for water, one of the hardest things to scale down well - mix detergent into the water to make the droplets in the water break into slightly (20-30%) smaller ones during a splash. BUT ALSO add an anti-foaming agent to minimize the bubbles that result from the detergent. 
Bonus #2: Cloud tanks can make awesomely weird billowing-smoke effects.

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