Glitter, glue, isopropal alchahol, & Food Coloring
To start with, take your jar and fill it about a quarter full with isopropal alchahol. Then, fill it to 3/4 full, and add some food coloring to get the color you desire for the base part of the glitter bottle. Warm water works best, to get everything mixed together without clumping.

After that, take your glitter and add it in. Remember, the more glitter you add, the less you'll see of the base color when it's mixed up. The finer the glitter, the more it will swirl.

You can even mix different glitters together, for new colors or effects. I like to mix a holographic-pearlecent glitter in most of mine, along with a color that goes with the base. If you're using small bottles, tiny funnels are your best friend at this stage.

Nect, you'll add the glue. You want to use a clear glue for best results. The more glue you add, the longer the glitter will float, but the less it will swirl. Experiment a few times to find the right consistancy for what you want.

Now add your lid and shake it up!

As a side note, once you get teh bottle looking like you want, you'll want to hot glue the lid down, to make sure no liqued gets out as you're shaking it up.
Here's an example of what I go for: