I use Photoshop for all my pixel art. I would recommend a program that uses layers.
Example of my pixel art:
Viewing post in what software do you guys use
Thanks! I don't have a portfolio site, but my Twitter is @osariongames. And if you want to see some more of my pixel art, check out: http://www.osarion.com/assetstore/assets/beat-em-up-game-template/