The built-in Maps application uses vector maps that you download en masse before us, typically divided up into regions. Maemo Mapper, on the other hand, is much simpler - it downloads raster maps (PNGs, typically) that it just displays on the screen. There are pros and cons of each type of map. There are a ton of other differences, like the fact that Maemo Mapper is open source and completely free. You can peruse Maemo Mapper's online help, if you like, or you can just install it and try it out.
And yes, Maemo Mapper can search for nearby POI, although the interface isn't particularly pretty.
