I've recently started an SGA thematic list in two parts for stories that either feature alien Pegasus cultures prominently somehow, i.e. both new and canonical human Pegasus peoples, but the aliens have to be visible as a culture in their own right rather than just being a plot device of "random angry aliens chased them to the gate" or "aliens made them do it" without the story bothering to explore the aliens' reasons further, and for stories with new non-human aliens, i.e. not stories about the Wraith or Asuran or Asgard... cultures, but first contact with new, non-human aliens. So far it lists about 75 stories, but I'm sure there are more.
At the moment the list is lacking John/Elizabeth stories in both categories, because I don't read that pairing myself, so I'd be grateful if J/E shippers could help me to make the list more rounded by pointing out any J/E stories fitting with the alien theme.
SGA thematic list: alien cultures and new non-human aliens