I don't mind filler arcs that much at all. Though, I generally define filler as an episode and/or arc in which nothing significant to the plot happens or character development and you can skip those episodes while still understanding the rest of the storyline. Sometimes, people use the term filler to describe an arc that wasn't based an a manga, if said series is based on a manga.
Anyway, I actually like a lot of the non-cannon arcs in the anime series I watch. I still prefer the DOMA and Noah's Virtual World arcs over most of the cannon arcs in Yu-Gi-Oh!. I also liked what I saw in the second half of FMA, including the movie. I don't really watch many other series where there are "filler" or non-cannon arcs, such as Bleach, Naruto, YYH, etc. since those series never really appealed to me for some reason. I think non-cannon arcs can be done in the right way, mainly if they're not dragged on for ages and there is a fairly good storyline to focus on, as well as character development.