Quite possibly.
There was the plot that linked Great Modron March/Dead Gods which was also subtly foreshadowed in 'Doors to the Unknown' and the allusions to Orcus in some other prior material.
The only really big one was the ongoing metaplot involving Duke Rowan Darkwood and his quest to the topple the Lady of Pain, culminating in the events of Faction War. Little bits here and there in a number of sourcebooks touched on and hinted at it all, and it was really, really well done IMO. Also it was fairly self-contained as a metaplot, not really impacting things outside of Sigil and the factions.
Thank god I ignored the whole Faction War shenanigans, talk about ruining a perfectly good thing.