Editing individual alpha pixels in pixel art is a torture with modern graphics programs. Atleast when GIMP or Photoshop, it's all not made for pixelation. But well, the reason why I'm complaining is that can't just edit my minecraft skin in the way and with the program I want. I'm a longtime GraphicsGale user, but editing alpha channels was also luck and experimentation. In the end I forget it and need to figure it out later. So I just can't get my head accessories transparent and also tried Paint.NET. It's able to edit them individually as it seems, but kind of stupid in the sense that it handles color-only or alpha-only selections. So if you use the fill bucket, there's no way of filling a color's alpha value but an alpha value areas alpha value and so on. It's totally garbage in terms of interface decisions. So guess what I need to do one day? Right, making a pixelation program. And I'll NOT use any GUI toolkit for it, it'll be made of pixel-perfect 2D rendering. And with tools that are able to react on different channels as you've set them. A good pixel art programs consists imho of a very basic set of things but combined in a versatile and color channel-aware manner.
Computer graphics sucks so hard when it comes to such things. *sigh* I wonder if I should check out Pro Motion instead of GraphicsGale. Atleast you can pay it with Paypal instead of stupid credit cards... The reason why I haven't yet got a full version of GraphicsGale.