Right now, the ways that you can win include closing the chaos gate and leave the chain, the ordinary chaos god ending, and the ultra endings. To my knowledge, this is essentially the full extent of the ways that one can "win".
I'd like to see more ways to win.
For instance, how about the "Immortality" win, where you close the gate and then get yourself petrified. As an extension to this idea, I'd like to see a wish for immortality result in the character getting petrified. The logic here is that you gain immortality by having yourself turned into a statue for people to look up to. There would, to my knowledge, be four ways to win in this way - wish ("immortality"), gorgon breath, eating a gorgon corpse, and possibly using petrification spell on self. Of course, higher points if you do it in either Terinyo or Dwarftown, with a special version happening if you do it on the magical island in the middle of Terinyo. Perhaps one also needs to be crowned in order to achieve immortality in this way.
Another idea could be to make it so that you can permanently close the gate, killing yourself in the process, by casting Earthquake (or using a wand of earthquakes) repeatedly while standing next to the gate itself. This would be a rather grim win, of course, as the idea is that you're collapsing the caverns of chaos themselves, which means you're destroying, for instance, Dwarftown in the process. The resulting extreme earthquake would basically radiate throughout the Drakalor Chain and beyond, causing much devastation. But it would still be a win.
Perhaps a third new way could essentially be stopping the incursions of Chaos by recruiting the powers of Law, an approach available to lawful and neutral champions (for Lawful champions, you unleash the powers of your gods. For neutral champions, you're bringing balance by pitting Law against Chaos). To do so, you must find a way to essentially create a Law Gate on D:50. Perhaps, to achieve this, one must have the Law skill, have a blessed Holy Symbol, a Potion of Balance or of Cure Corruption for Neutral and Lawful champions, respectively, and must have one of each of the non-magical gems (not the glasses, just the ones actually worth something). placing the potion and the gems on the ground within the main chamber of D:50 and then 'U'sing the holy symbol would open the new gate. However, one must be very careful, as this does not end the background corruption, and increases the monster generation rates as you return to the surface. This would not be eligible for the "Immortality" win.
As a special variant of that idea, if one is a Paragon of Order when one opens the Law gate, and one then eliminates almost all corruption from one's body, one can then enter the gate and become an ordinary lawful god, in counterpoint to the ordinary chaos god ending. Obviously, one challenge with this would be getting the Law skill (assuming you're not a lawful Paladin), since you can't attack Hotzenplotz in order to kill him.
One last "win" could perhaps be designed as a challenge of a different sort, having some similarity to the Cute Puppy quest. Specifically, one must get to D:50 within a very strict time limit - the exact limit would have to be chosen carefully, of course. Once on D:50, within that time limit, one finds only Fistanarius resident on that level. Kill him before the time limit is broken, and no other monsters get generated on D:50. Once the time limit hits, if Fistanarius is still alive, monster generation on the level happens rapidly, and one must achieve one of the other wins. If Fistanarius is killed in time, one can close the gate using the levers and leave, and rather than simply stopping the incursion, you are credited as having stopped it before chaos could gain hold in the world. If one manages this while still entering the chaos gate for a special ending, they combine, having blocked the incursion and also killed Andor Drakon.
The only idea among those that I'd like would be the Earthquake thing. A requirement, say, of casting Earthquake a total of five times with a Mana and Willpower of at least 30 while standing directly on the chaos gate square, surrounded by a dozen balors plus Fisty, unless they've been chased away. The idea does have some charm, flavor-wise.
Unfortunately, I think changes like this are going to be unlikely. We've been waiting for simple bug fixes for a very long time, after all.