I personally wish there were a few more options to sort the palette by instead of lightnes and hue/lightness (ascending/descending sub-options, sorting by hue alone, saturation, etc. would be helpful),
The 'ascending/descending' option is unnecessary -- just use 'Invert' or 'X-Invert' afterwards if you want the result to be descending-order.
(I think the typical usage of 'Sort' is not on the entire palette, but on the colors of a specific ramp. Personally I find sorting the entire palette feels orderly and pretty, but unless the palette is fairly small, it mainly just makes the picture harder to edit. YMMV)
but perhaps I could just extend it with a Lua script (I *am* a computer scientist before an artist, so that should be an easy thing for me)
Actually, SuperSort, from Dawnbringer's
huge package of Lua extensions (that url should be accessible once PixelJoint forum goes back up..), may do what you want.
It has the option to sort by any of:
* histogram
* brightness (finetuned formula)
* Hue-> Bri->Sat
* Sat->Hue->Bri
* Sat->Bri->Hue
* Bri->Hue->Sat
and the option to automatically remove doubles.
..You may also like the overall package from the point of view of providing a big set of examples how to write plugins.
After playing around with GG and this, I think this is definitely a better piece of software in most respects, and definitely when it comes to tons of feaures.

Oh, you might want to check your 'cursor' setting (under 'skins'). I recently found that switching to 'transparent' made it much easier to see what I was doing.