How to hide folders on a windows portable disk when viewed on mac os x
There are two ways I know of.

You can start the folder's name with a ".", as in ".folder". This will hide them on any Mac, though other Windows can see them.

Or you can use the Terminal command "chflags hidden ~/Documents/folder", replacing that place with the path to whichever folder it is you want to hide. But I don't think this would hide them when connected to another Mac.

You might want to look into using an encryption service like TrueCrypt.