I might have misinterpreted your question, but a 50mm lens is half the focal length, and therefore has twice as wide an angle of view as a 100mm lens. So if you take a picture of a subject with both lenses then there will be twice as much information in the photo taken with the 50mm because of the wider angle of view.
If both lenses are macro then we need to know what magnification each lens has in order to compare the two. Assuming that the lenses have comparable magnification then the difference will be that you can be farther away from the subject with a 100mm lens to get the same amount of information in the photo. If you take photos of bugs for example, you really have to get very close to the bug to use the macro function, maybe inches away. This would interfere with lighting and maybe even disturb the bug. With the 100mm lens you would be further away and get the same angle of view. If you were taking macro shots of venomous snakes you could get even further away using a 200mm macro lens and still get a good macro shot. That would keep you out of the hospital - mostly.
50mm lens are the easiest lenses to manufacture, therefore they are generally the least expensive of all lenses. The longer focal length lenses are much more difficult to make, so a true macro 100mm will be relatively expensive. This will depend on other characteristics of the lens though, such as maximum aperture, whether the lens has fancy things like image stabilization, and of course the maximum magnification.
Well, the 100mm will have more versatility and you'll find these are among the sharpest lenses in a manufacturer's portfolio of lenses.
Remember though that, if cost is an issue, you're not compelled to buy brand new. There are thousands of excellent used gear out there and the optics of old lens really haven't been improved upon that much.
Here's an image from a 25 year old 105mm Nikon Macro fitted to a modern DSLR:
Thanks guys. I am always showing my friends these fly shots of yours Mark to show what macro lens can do
Have no particular purpose to use macro though. A bit of this and that maybe. Will start looking for a used one and see for what money they go compared to new ones. Is there any other place apart from ebay to look at used ones? There will still be some time before i get enough money as have just purchased a sigma 17-70 with os last week.
Well if you live in London you're spoiled for choice. If you're a Canon buff for example, check out London Camera Exchange The key point in this sample (even though this particular sample is located at a different store than London) is that it has a 1:1 magnification ratio. This is the as good as you'll see in a macro lens because it means that the object will be exactly the same size on the film as it is in real life. On top of that it has a fairly wide, if not earth shattering maximum aperture.
The thing you need to remember though, is that if you don't have a specific macro shooting goal in mind then perhaps you don't really need a dedicated macro lens. Instead, you should think about getting a more general purpose lens that also has macro ability. That way the lens becomes more useful to you. Some zoom lenses have macro ability although they may not have as good as a magnification as 1:1.