Are you talking about 2 wet flies, or 2 dries, or 1 and 1?
If it's 2 wet flies and your nymphing.. what I do is tie the first fly on with a surgeon's loop - it will leave a small loop/tag end that causes the top fly to "stick out to the side" from the tippet - giving it more action in the water.
http://www.killroys.com/knots/surgloop.htm
12" - 16" under that I will tie the bottom fly on either with another surgeon's loop or a regular clinch knot. Typically I've been doing a second surgeon's loop because for some reason my clinch knots are always slipping and it's very frustrating to lose fish over and over again because of a bad knot.
http://www.killroys.com/knots/clinch.htm
I've never tied 2 dries on so someone else can answer that for you.
With a "hopper/dropper" combo you can do something similar. I think the recommended setup is to tie the large hopper on with a clinch knot, and then the dropper fly to the bend of the hook of the top fly with another clinch knot.