Stitches is almost impossible to find, if he's not inside his house. There has been a few times I couldn't find him anyways for days. Usually when he's not at home he'll be looking at fish at the museum, any other time he vanishes. I used to have the same problem with Rosie, but it'd only be for a couple hours.
Oh geez for me it has to be My Peppys and Snooties Dx Ankha may not be permanent but must she be such a shopaholic diva??!! Really Ankha stop hiding all the time And even though I love Rosie, she is always in my emporium, can she stop shopping too for just one minute of my time to find her xD
It switches up. Lately it's been hard for me to find Deli. At one point there was an entire week that I didn't see Tom, until I checked out the aquarium in the museum.
In each of my towns, it's the ducks that are hardest to find. Molly and Quillson are never where I can see them and I like to check Molly each day to make sure she isn't thinking of moving.
For me, it changes which ones do that. Sometimes I'll go weeks barely being able to find a certain villager (or villagers, sometimes), then they're suddenly everywhere and another one disappears. If I really want to find them, I'll usually try looking in all the shops and museum rooms. They tend to be at the museum very often when they're missing.