Have characters which keep turning up twisting and turning the plot off screen.
When you need filler, make episodes which run parallel to previous ones, but focusing on these largely off-screen characters, giving a greater insight into deliberate mysteries and plot holes of previous episodes.
This could work really well with "loads of characters with superpowers" shows like Bleach, Naruto, or Darker Than Black.
Now just for a moment, where there was one where these fillers actually revealed the setting to be different to that of the standard ones, for example, lets' say the main characters were in some kind of high fantasy setting, but in the filler, it's revealed that its' actually a product of the main characters' heads, that they're actually sanatorium patients, that these "Filler characters" are the staff who just want to keep them occupied out of sympathy, or enjoy messing with them, or humour them to make things easier.