Soy yogurt is definiately available for sale, so there MUST be a recipe out there to make it at home. *strokes non-existant beard*
People have mentioned some really great ideas for re-using the cups!
I have a couple more suggestions, though.
If you want to do the planters, but are running low on space, you could string the cups together and hang them. The plastic is fairly thin, so you should be able to use a hole punch to make a hole in either side of the cup, then pass the string down through the cups from the inside of the hole out, and just knot the string/twine outside the hole to keep them from slipping down.
Also, like you said, I don't think burning candles in them would be a good idea (melting plastic smells AWFUL >_< ), but they would make awesome candle MOLDS. You can melt down bulk wax or the remains of used candles in a saucepan, then pour the hot wax into the cups. Line the cups up next to each other, then tie lengths of wick to a pencil and lay the pencil across the cups so that each cup has a wick down through the center and allow the wax to cool and set. Then you can easily cut/rip the plastic away, and voila! Just snip the wicks off under where they tie to the pencil. You could use the really big yogurt tubs and put three wicks in (in a triangle) for a great pillar candle with three flames. Sometimes it helps to tie the bottom end of the wicks to a small metal washer to weight them and keep them straight and centered.
Here's a rude diagram incase I didn't explain myself well.
Lastly, you could always decoupage the cups and use them to hold things. Any small craft supplies like buttons or sequins or glitter, etc . (or larger things if you use the larger containers!)