My only rule set in stone is that I don't have any rules set in stone. I have some guidelines I follow, like submitting exclusively to magazines. Part of it is instinct and just getting to know a market. Some magazines want you to query after a certain point (Strange Horizons, Beneath Ceaseless Skies, for example), and if you pay attention, you'll realize that these magazines actually mean it! You gain nothing by waiting. I queried a well known magazine twice because it was taking a long time, and with the second query, I received a polite personal response from the editor (that included an apology) and an inside scoop on what they were currently looking for. You can bet I quickly followed that up with another submission. You kind of have to learn through experience and get to know each market and how they operate.
I don't use Duotrope when deciding when to query, and I don't recommend it for query purposes! I know from experience that some of the stats are not correct for some of the magazines--that some magazines are much slower, and some faster, than the average response times listed. One reason is that it's different for each writer. Since I've been making a name for myself (or, perhaps, just writing better stuff), my response times have slowed at some magazines (as stories are held longer for consideration), and sped up at others. My stats seldom match Duotrope average response times these days. So unless you feel you fit squarely in the "average" (if you can figure out what that is), querying based on Duotrope is risky! I enjoy checking in on Duotrope with some markets, though, because it can indicate when a story has passed into a new round of consideration. But it's far from an exact science.
When in doubt, do what James Ritchie advises and work on a new story. Sometimes it's a good idea to give an editor time to work through the slush pile (which can vary widely from month to month in size).