Arrgh!! This makes me so mad/sad. I have played only the demos of the Geneforge series, yet I immensely enjoyed each one. Neither A:EftP, A6, or Avadon run on my computer (Windows XP), so I can't rightly judge for or against those either. Also, I've only played the demo of Nethergate and haven't the faintest clue what this talk of Nethergate: Resurrection is.
How long will this poll be up? Once I buy all the Geneforge series, Nethergate, and all the Exile games, buy a better computer, and play through each of those games, then I can give you an honest answer.
For now, A3 is my favorite. Then A2, and then BoA.