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On the arcs question, The main 4 question and 4 answer arcs were animated (along with one additional anime only arc to fill in the things left out of the first season that needed mentioning for the rest of the story to make sense).
The OVAs cover four more arcs (the Cat Killing Chapter from between Season 1 and 2 I suppose could be seen as an OVA arc). Three of the arcs are more or less random stories that don't really effect the main plot and could be played for humor. The meat of the current OVA series is one last arc that is effected by the main story..the epiloge I guess it could be called. The OVA's where not animated with the rest of the seasons because they didn't tie into the main plot line of the mysteries and the last three episode arc rounds out the story, but was not part of the story proper.
Also the VNs were released one arc at a time for the most part, aside from the comedy stories were sometimes added on to a disc for the main arcs. the ninth arc was released last with one or two short comedy arcs, but was not a question or answer arc, thus wasn't needed in the main two seasons I suppose.
As for the manga, I think the manga thread has a listing of all the various arcs that have been realeased (and translated so far I supppose)
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