NewIcons uses a newer icon library that allows use of icons with more colors - GlowIcons and most other recent icon styles are all descended from that library. I find the NewIcons themselves very aesthetically unpleasing, though.
If you ever come across an icon that's just a tiny little square, it's because the NewIcon library isn't installed for it to render correctly. You can install just the library and appropriate system patches for compatability purposes while still keeping your MagicWB icons.
I use 3.9's GlowIcons primarily, with 2.x-style icons in other places.
