Sigma 70-300 APO or 100 mm Canon ?

One factor in making your decision should be the lighting conditions under which you shoot macros. The Canon is a faster lens and will operate better under lower lighting conditions. I haven't played with the Sigma, but I image that at 300mm and 5.6, you're going to experience quite a bit of camera shake which equals motion blur. Not a good thing in a macro. Furthermore, at $200 (if I'm looking up the right lens), you get what you pay for with the Sigma. Unfortunately with lenses, the general rule is that the less you pay, the less you'll get (with the exception of the Canon 50mm 1.8 which is an exceptional deal).

Personally, I'd go with the Canon because I have a weak spot for prime lenses.

I'd skip the Sigma and get the Canon. Aside from the build quality being better the Canon will be a better macro lens. According to the specs I looked up on B and H the Canon shows the magnification at 1:1 whereas the Sigma is only 1:2.

I own a Sigma 24-70 "Macro" lens and yes it does get pretty macro-ish but it's not like I'm able to look at bugs real close. Although my lens is only a 1:3.8. It's not terribly sharp either.

The biggest difference in Canon's lens is the Image Stabilizer, which is worth about 2 to 3 stops of extra lens speed. That's a lot with a long lens when the light is poor. You'll be able to produce sharp images with the Canon in lighting that would be impossible for the other two lenses. You have to consider your needs. If most of your shots will be under good lighting, you probably should not spend the extra money, but if you must make the shot even under poor conditions, the Canon is the way to go. I've shot sporting events such as crew and motor racing with Canon IS telephoto lenses. The stabilizer makes all the difference when the day is dark and stormy or sunset is fast approaching and the money shot still has to be made.