What version of clonezilla live should I use?

The version depends on your hardware, not on the operating systems you have installed. for example, you have Windows Vista 32 Bit and Ubuntu 12.10 64 Bit, which means that you have hardware that can either use 32 bit or 64 bit software. With that in mind let us look into your list:

clonezilla-live-2.1.1-7-amd64.zip
clonezilla-live-2.1.1-7-amd64.iso
clonezilla-live-2.1.1-7-i486.zip
clonezilla-live-2.1.1-7-i486.iso
clonezilla-live-2.1.1-7-i686-pae.zip
clonezilla-live-2.1.1-7-i686-pae.iso

Since what we want is to burn the image, we go with the .iso files which leaves us like this

clonezilla-live-2.1.1-7-amd64.iso
clonezilla-live-2.1.1-7-i486.iso
clonezilla-live-2.1.1-7-i686-pae.iso

Since you have a system that supports 64 Bit you can use the clonezilla-live-2.1.1-7-amd64.iso version. You can also use the i686-pae but it is better to use a 64 Bit version of a 64 Bit supported hardware.

Now, after downloading the 64 bit iso, do not worry about cloning a 32 bit Windows or Linux OS. Like I said before, the version to download depends on the hardware. So with the 64 Bit version you can clone either a 32 Bit version or a 64 Bit version of an OS installed without any problem.