Yes, we use QGIS instead of Arc for basic GIS debugging and manipulation. My non-technical partners and employees use it to manipulate shape files to make them compatible with formats we support for imports etc. And I regularly use QGIS to help understand random GIS data we get. It lets me overlay GIS data on a Google Map base layer very easily which is often helpful.

Most of the GIS stuff we do uses programming libraries that leverage gdal/ogr/proj - basically the same stuff QGIS is built on.

We also use MySQL and its limited spatial functionality. We use PostGIS and SpatiaLite too. SpatiaLite can be a great way to get a lot of data into QGIS in a form that can be queried pretty efficiently.