If you have a good idea for an arc, go for it, but make sure the arc is not too long to be able to get back to the classic one-pages if neccesary.
Some gag-a-day use short arcs to make different jokes related to a situation. Ex: "The gang go to the beach", so the next few updates are about the wacky situations that happen on the beach, or maybe two characters make a dumb bet that gets solved after a few updates.
and this goes without mentioning running gags or a brick joke
There also have been cases where there is a short story arc made for the finale, to give the readers closure.