I have two aquariums that are on stands about the same height off the floor. Tank 2 is about 1ft shorter in height than tank 1 so I can use a siphon  to move water from tank 1 to tank 2.  I use a pipe that is about level with the bottom of both tanks.  The flow rate though is really low. What I want to know is if I were to get a longer pipe and run the pipe from tank 1  to the floor then back up to tank 2 would it have any effect on the flow rate ?  Would the water being pulled down by gravity speed it up or is that not much of an effect when using something like a siphon to move water ?
I'm trying to find a solution that does not involve using a pump. Sometimes the water contains baby fish that are very tiny and any pump in the path would kill them .
		
		
	 
u might run into problems with the bottom tank overflowing if the bottom pump wasnt pushing enough water up.
OR, if your bottom pump was too strong, you will overflow the top one. 
You need one of these on both tanks, so they stop siphoning when your tanks reach a certain level:
http://www.fosterandsmithaquatics.com/product/prod_display.cfm?c=3578+3579+18358&pcatid=18358
Then you get a pump to just push water up.
As ruby says, the top siphon will draw water below, as it draws too much water and gets low, the siphon will stop.
This will prevent the bottom tank from overflowing. 
Then the bottom tank can push the water back up with a pump as long as that pump isnt pushing more water then your siphon can bring down.
Remember you dont need to be = this time, just make sure your siphon is > then pump.
	
		
	
	
		
		
			Yes that's one way.  Predrilled tanks are great for that otherwise one needs to fit overflow boxes.
		
		
	 
Ruby that picture has a high placed intake like the unit i showed above. 
That PCV which sticks up only collects water up to a certain level, and once the water line goes below that, it wont draw in any more water.
Also using that kind of design is VERY NOISY.
Ive had it... its horribly noisy.
Model im assuming you want a refrigium addition to your tank or a wet dry filter system?