I don't know much if anything about macro, but the way I read your post you're mainly asking for advice in post-processing, right?
I'm not sure post-processing in macrophotography is much different than in another genre and I guess people use more or less the same tools, albeit, as Clyde suggest, sometimes pushing the sliders quite a lot! lol
I guess you already know but the main pieces of software out there are Adobe's Lightroom and Photoshop. That's not free and I doubt many will encourage piracy openly in a forum like this one...
If you're looking for free alternatives, I started a thread some time ago... here it is: http://1x.com/forum/editing/388/1374354935
From what you say "remove objects", "work only on some areas" you're probably going to need something with layers and masks and local editing possibilities (clone, dodge/burn... etc) like photoshop or gimp.
From the little I know by looking at the macro gallery here at 1X, if that's the look you want to get, you might want to play with:
- sharpening
- white balance and saturation for punchy somehow unrealistic colors
That's my 2 cents, waiting that someone with more knowledge comes around ;)
Cheers,
paco.