So far, I have a favorite shipping per saga, by virtue of how strong hints were/what could/might happen, character-wise.
Ash x Misty
Tracey x Daisy
Falkner x Janine
Brock x Lucy (despite the fact I'd love to see Holly x Brock x Lucy OT3)
-So far, Lucy is the most memorable CotD that mutually like Brock back.
Wobbuffet x Kirlia from Fear Factor Phony
-I'm just glad to see some character development for Wobb; it always strikes me as a wallpaper.
Reggie x Maylene
-Paul as factor. He dissed both these two during the Sinnoh season.
-vs Team Galactic. Both fought them off.
James x Gardenia -their respective affinities for Grass types went far (not yet to the extent I'd like) and the fact Gardenia offered to train his Cacnea clinched it for me.
Conway x Dawn
Zoey x Candice -
Holly x Brock (even though Holly x Brock x Lucy OT3 is the best for these 3 together)
Elesa x Skyla
-like I said elsewhere before, it's the symbolic Thunder and Lightning and the crazy amounts of L Yay!