Board Thread:Questions and Answers/@comment-31417419-20181008074350/@comment-27815744-20181008151146

Both paint.net and gimp can easily fill in disconnected areas using select and shift fill, but I just find paint.net more user friendly. Gimp has more features but unless your making textures these features mostly go unused. You can also get addons for paint.net that add much of the features from gimp. But apparently not convert to alpha... that would be too much to ask (me being salty).