This answer is purely speculation so if somebody else posts an answer that has an official source, please feel free to accept that answer instead.
- 365 (Season 2): Some of these events take place before, during, and after season 1 if I remember correctly. So basically they're saying something like "we're going back to then and showing you all 365 days of their year!" (except they aren't literally showing you all 365, just more of what you saw in season 1)
- Hoshimittsu/☆☆☆ (Season 3): Three stars for season three
- Honeycomb (Season 4): There are six sides on a typical honeycomb, and there are six girls living at Hidamarisou. If this is the reasoning, they could've used this title for season 3 as well though.
As Logan M said in the comments, SP just stands for "special" (as opposed to a TV series). I don't think there is any significant meaning beyond that.