I just used a regular house paint brush. I had several hundred to do so I was not going to mess around with smaller brushes. The plastic sucked the paint right in. No loss of detail at all. I could dry-brush them or something for added detail, but I am happy with how they look and really have better things to do than fiddle with hundreds of tiles. Tiles still lock in ok. It is a bit more difficult sometimes, depending on the tile. But to be honest I really don't notice a difference.
I guess I could have airbrushed them, but I wanted the color to match the mat perfectly. I did airbrush the water tiles. Used Tamyia Medium blue for Depth 1 and Field Blue for Depth 2. However I really don't use the water tiles. I found the MDF hex tiles from Gamecraft Miniatures were a better fit. I know some people do whole tables with Heroscape tiles. I neither had the desire or tiles for such a project. The hex mat works fine and it easier for me to store.