Since I'm starting to develop games, I'm using Adobe Flash to make the graphics. And now, I'm also used Adobe Illustrator and Inkscape to make sprites and BGs.
Currently, pixel art is not my style for now.
For the musics, I'm using FL Studio.
For the SFX, I found them in some games I have (the most common sounds) and from free assets platforms like FreeSound. I'm sometimes make SFXs using Audacity, FL Studio, sfxr or bfxr.