There is a new piece of software known as Pixelorama by Orama Interactive. It’s completely free. And there is an online option too, if you don’t wish to download anything.
It has the capability of making grids for both isometric and rectangular grids.
It also has various tools for drawing, such as making rectangular and circular shapes, a curve tool, a line tool, and a shading tool. It has layer support, and you can animate with it. It even has a 3D model importer.
It does offer support for extensions, effects, and filters. Among those effects you’ll find drop shadow, which may offer the shadow you are looking for.
If you wish for a more simple interface than Pixelorama, you could try Piskel. It also has both online and offline options, and includes many of the tools in Pixelorama, such as animation, but you will be missing out on extensions, filters, effects, 3D importing, etc.
It still is under development.
All options listed above are open source software.
(P.S. Sorry for being so late. I posted this answer just in case it helps anyone.)
