I make all my graphics in PhotoImpact, which is actually a photoshop like program.. but you can turn down the anti-aliasing to make it draw like MS paint. It has all these cool options and brushes that are very useful for pixel art. It even comes with a GIF animator that I use for all my transparency needs.
http://www.ulead.com 
I don't understand why everyone is always like "100% MS PAINT!!" other programs can do pixel art 10 times better
WITHOUT filters :O