Originally posted by Anarchist Jurisdictor:

I pretty much just have portals named after the biomes or bosses they go to

"Elder"
"Bonemass"
"Swamp1"
"Swamp2"

etc

You name the path that connects the portals, not the portals themselves. This lends to naming it after the function like Nox does.

This assumes that you use a hub though, right? So you never have to name one half of the portals. It's just assumed that it is your hub.
There must be other people who use more of a subway map style.