Damned if I know! I tend to do a few different things. In my most recent Kate and Fowler story, I listed Peter as a character in my journal (he has one line), but I didn't tag him on AO3, because, as you said, someone looking for a Peter story wouldn't be satisfied with that.

However, I have tagged him when I considered him emotionally important to the story. He appears only briefly in Weigh Your Eyelids Down and Living in a Kind of Daydream, but I consider him important in these stories. Same problem with Wish You Were here. Peter and Mozzie have one scene each, but I consider those important scenes.

I have an even bigger problem tagging pairings. What's the line between tagging a story as gen, tagging a story as both ship (het/slash/whatever) and gen, and when is it a pairing fic? There are certain pairings that are frequent background parings. When I go looking for Peter/El or Neal/Kate fic, it's hard to find actual pairing fic. But I understand why people do it. Weigh Your Eyelids Down is tagged as both Neal/Kate and June/Byron, despite the fact that it's quite gen, because those pairings do appear in the story.

A background pairing tag would be a godsend, is what I'm saying.