I think fan service should be made by the fans, period. Unless the creators can spend a whole episode introducing and supporting all the major ships out there. It would be interesting because they'd all be canon. :o
I love fanservice and I don't think it should ruin a good plot. Both should go together, however since this is difficult to do, comedy shows are a good option to include it just because it really goes along with most of them.
Time and place, it is as simple as that. I don't normally like fan service but I think of Blame! Academy and that reminds me that some times it can be good.
Ex. Anime spamming panty shots instead of story building events