The Alwan ending in Geneforge 5 is one of the greatest endings I have ever seen in any game. Ghaldring dies, you retire in glory, barred creations go extinct, Terrestia is reunited under the Shaper banner, Shaping gets under control again, the Geneforges are drained, and the Trakovites disappear.
In the same game, the Ghaldring ending is horrible. You do all that work to overthrow the Shapers, only for it to be rendered meaningless in the end as Ghaldring gets overthrown and the shaping laws are reinstated. Makes you feel like your hours of gameplay was all for nothing
AS for other games, the Geneforge 3 Shaper ending is really good. Like you, the Geneforge 4 Rebel ending gives me a "WHAT HAVE I DONE" feeling