In my studio I use Inkscape, Gimp, Blender, and Zbrush to make 2D graphic tiles.
Most of my recent work has been only done in Blender, using Gimp for a small tweak here and there.
As far as Seamless tiles are concerned I have been using Neo-TExture Edit. It renders 100% seamless textures.
If you have a little bit of money you might want to replace NeoTextureEdit with Genetica.
To use Inkscape for pixel art I make my sprites 256x256 and the pixels I make 32x32 squares with the grid turned on. Make sure you turn off Anti-Alias or you will have problems with colors bleeding. Then scale them in Gimp with the scaling mode set to NONE.
Recently I made my own in-house pixel editor. It has the cool features of GIMP and Inkscape , ,plus a couple I have never heard of before. My favorite is the ability to move the pixels around freely, and the way the color changes can always be recovered while animating.
You can find one version in the Scirra arcade, but the arcade does not seem to allow POP-ups... So i need to release a node-webkit version.