How interesting, I'm in the same camp and much prefer story driven episodes versus those that are stand-alone. Which is probably why I like shows such as 24 where every episode is pretty much story-driven. I haven't found a solution to weeding out the filler episodes without spoiling things. However if you want a site where you can check out both short and long summaries of TV episodes,
Television Without Pity is a good one.
I would think that there'd be some website out there dedicated to this issue (e.g. for popular shows listing which episodes are story-driven, standalone/filler, or in between). Maybe there is...though I've never looked for one.