I use a custom engine, using Unix makefiles to build it. It is using freeglut behind the scenes to create windows and handle the OpenGL context.
For graphics, I use Gimp for 2D (usually textures), and sometimes Inkscape. For 3D, I mainly use Blender.
For audio, I’m using Musescore to create themes, I’ve tried several others for sound effects, but haven’t really decided on one.