I recently looked at the state of master palette editing, and it's still pretty annoying to do right.
Either you do a lot of manual manipulation of individual pixel colors, or go to unusual lengths to get colors out of the image, into a freeform palette format (such as GIMP Palette) that can be rearranged readily.
Editing the palette directly using a dedicated indexed-palette editor is also unreliable, as the 24bit input format makes the order of the indexed palette unreliable and usually wrong.
I wasn't happy with this state of things, and GrafX2 is my pixelling tool of choice, so I made a script that you can install into GrafX2.
It fixes the misarranged indexed palette that comes from importing a 24bit palette, in a single step.
This effectively allows you to handle indexed palettes and 24bit palettes (ohr standard format) with equal ease.
You can use the standard color tools (Curves, Levels, Color Balance) etc in GIMP/PS/etc to adjust the palette's overall characteristics, and GrafX2 for editing individual colors, building gradients, and rearranging easily.
In short, loading a 24bit palette in the standard OHR-recommended format into GrafX2 results in this:

(note the difference between the image layout and the indexed palette layout)
After invoking the script:

(layouts match, you can edit the palette to your heart's content and both OHRRPGCE and GIMP will understand it.
After doing a 24bit edit in GIMP, all you'll need to do to get the updated palette is 1. reload the image, 2.run the OHR palette arranger script.)
I've also clarified and updated the GrafX2 page on the wiki, and am planning on doing some screencasts on the OHRRPGCE-related topics covered there (animation, advanced tile editing, master palette editing,). Tell me if you're interested in anything particular and I'll see what I can do.
You can get the script from here: http://rpg.hamsterrepublic.com/ohrrpgce ... script.zip
Installation instructions are included in the zipfile. Feedback from Windows users is particularly appreciated .
Thanks to The Wobbler -- spotting his HoTOHR request inspired me to take care of this.