If you're willing to compile it, Aseprite is a great option as well.
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Take a look at an add-on for Blender called BoxCutter. It is a fully featured Boolean system and a slicer that is said to be more powerful than Booltool and Hard Ops combined. BoxCutter 6 is only compatible with Blender 2.78 and above.
Details on different versions:
Here’s some information on how the add-on works:
With every update we seek to enhance the user experience. And make Blender not only more welcome for long time users but approachable from others who have never seen this before. We don’t want buttons and features. We want simplicity and to offer it in a way that is sensible and intuitive.
When you start boxcutter there is a border. If you press alt + shift + mmb on a face. The view will align to that face. This is something I wanted to add to hard ops as well but differently however that may come at a later time.
This tool is invaluable to making angled cuts and and comes in handy for alignment related issues. I use this all the time and cant wait for it’s next level.
Boxcutter now has mirror. This is a big enhancement and was a welcome addition to Boxcutter. In the D menu you can select the axis (holding shift) and select multiple axis.
Before I would cut on one side and mirror to the other using Hard Ops (alt + x).
Enabling the a mirror axis on the D menu will allow mirror cutting.
Non Destructive Changes
There have also been changes to the format of the D menu. This should make it easier to understand / use.
Pressing R during drawing will rotate the object the amount of degrees specified in the D menu.
Developed by AR, MX, JL, IS, and endless python mercs.