I'm having issues with the tools I use.

Mainly I like to sketch and draw in The GIMP, but its paletted graphics support is primitive. Also, it has on occasion reordered the palette on me, ruining a couple of images. :( This is a big problem, because for my game dev uses, the 256 color palette is divided into 16 banks of 16 colors.

With an app like Usenti (http://www.coranac.com/projects/#usenti) I can easily work with these palette banks, looking at any given one. The pixels in the image are interpreted as being only among the "first 16" colors and depending on which palette bank is selected these colors APPEAR different. Switching between Usenti and GIMP works for the most part. I have a workflow going.

One problem is that Usenti doesn't play nice with Wine under Linux, so I have to be careful which features I use or the pixels will be corrupted. This and the GIMP "reorder" issue above ruined stuff for me, and I'm eager to see if YY-CHR (http://www.geocities.jp/yy_6502/0yychr.html) can replace both apps. I just need to figure out how to load my palette as it handles those separately from images.

Now... what are your preferences, and do you know any other tools that have game-related palette features? :)

Possibly. :) I gave it a try (though not the latest version) and gave up in disgust over its weird user interface. It's like being thrown back into the 80's, like a bad competitor to Deluxe Paint. 

But I might give it another shot, though from the wiki I couldn't tell if it did palettes the way I need to. For now I managed to move my stuff into YY-CHR and it works remarkably well.