First things first, there are no silly questions. Trying to figure out any letter coding can be quite a task, and if you thing it is difficult with lenses, try it with Japanese motorcycles...
'Micro' is Nikon's word for macro-capable lenses. It's just their thing, if you see the word 'micro' on any lens made by Nikon, it means that it can be used for macro work.
Now, judging from what you have put down about the two 60mm lenses, here's my best guesstimates:
60 AF-S micro f2.8 G ED = 2008-present model (Nikon 60mm AF-S f/2.8 G ED (N) Micro-Nikkor)
In case you care, this means a 60mm micro(= macro)-capable Nikkor(=Nikon) lens with AF(=autofocus ability), S(=silent wave motor, making less noise while focusing) G(=gelded aperture ring, meaning NO aperture ring), ED(extra-low dispension glass) and N(=nanocrystal coating) features. The 'N' is actually printed on the lens and usually does not appear with the rest of the name.
60 AF-S macro f2.8 D = 1993-2008 model, with several cosmetic and functional differences from the aforementioned 2008-present model which replaced it. (Nikon 60mm AF f/2.8 D Micro-Nikkor). It is almost identical to the 1989-1993 non-D model which it replaced. There is no 60mm AF-S micro lens with the 'D' feature, and given the 'macro' (instead of Nikon's 'micro') word used I am inclined to believe that this lens is the older model. The 'D' feature has to do with flash use and exposure settings, an it is not menioned anymore, although all newer versions of Nikon's lenses (like the newer version of the 60mm micro) have it.
Here's a brief rundown of the differences. I will use AF-D for the older lens and AF-S for the newer one.
Cosmetic/Appearance/construction:
1.AF-D: white lettering, AF-S gold lettering.
2. The AF-D is about an inch shorter when fully retracted(not-zoomed in) and about the same length with the AF-S when fully zoomed in. The AF-S does not change size, as it is an IF (internal focusing) lens and anything that need to move for focusing or zooming purposes does so internally.
3. The AF-D is somewhat heavier than the AF-S (more metal parts like the filter threads). Do a google image search (with the correct names) and you'll probably see that they look quite different from each other.
4. The AF-S looks more like your 18-105mm, while the AF-D looks a bit 'older'.
5.The AF-S does not have a manual aperture ring (remember it is a 'G' lens) while the AF-D does. It really does not matter, unless you need to use the lens with film cameras someday. The D5000 will not let you use the feature anyway, and you can only control aperture settings (f stops) electronically (the 'A' mode on your top dial if I am not horribly mistaken).
Functional:
1. The AF-D has about an extra inch(and then some) of working distance (meaning that you can use it for full macro one etxtra inch further away from the subject) in comparison to the AF-S. In comparison, a 105mm will have about a foot of extra working distance form both with obvious results in your ability to properly light your subjects.
2.The AF-S is much easier to switch from Auto to Manual focus as you just need to twist the ring. The AF-D has a lock you need to operate before switching to using the manual focus ring. It can be a pain underwater.
3. At f/2.8 the AF-S has noticeably more falloff (dark corners) than the AF-D.
4. At f/2.8 the AF-S can be noticeably sharper than the AF-D, which is still quite sharp and ouperforms most third party 60mm macro lenses.
5. The AF-D can be significantly cheaper than the AF-S.
Hope this helps.