VOY era: The crew encounter the flourishing Silurians who left Earth a long time ago.
Wasn't that basically the episode Distant Origin?
Okay, seriously though, most of your ideas would be undoable for a simple reason: IDW can't do anything with DS9, Voyager, or Enterprise. Their license only covers TOS, TNG, and the Abramsverse. They did have a license to DS9 but due to low sales of the Fool's Gold series, they let the license expire and haven't renwed it. Under certain circumstances, they can use characters from the other shows (like various Voyager cameos in the TNG Hive series), but otherwise, those shows are off limits.
Also, since IDW has never done anything with the Daleks, one can guess it's because they don't want the added burden of having to deal with the Nation estate over the rights. A crossover is problematic enough trying to appease two different studios, a third party, particularly one as notoriously difficult to work with as the Nation estate would be avoided at all costs. True, they had to seek permission for the Cybermen, but the estates of Kit Pedler and Gerry Davis aren't as picky about the Cybermen as the Nation estate is about the Daleks. It's for a similar reason they didn't use the Abramsverse for this, Bad Robot would then have had direct supervision over the project.