1. Write another story instead of worrying about the submission. Seriously.
2. What do the guidelines say? If the guidelines say six months, then six months it is. If they say two weeks, so be it. If it’s an anthology, do not expect to hear back from an editor at least until submissions are closed.
3. What does Duotrope say? Duotrope often has return times. While this is useless for anthologies, it can give you a decent idea with magazines. For example, the reported response times for Analog match my experience.
3. Did you get a “receipt” e-mail? Many online submission sites will send you a “we got it” e-mail. If you did not get one of these, then you’ll want to edge towards the low end of the response time. If you did get acknowledgement of receipt, then be patient. Longer often means that they’re actually looking at it seriously.
4. Barring any other guidelines, 90 – 120 days minimum. And let me just say that if you decide to inquire at that point, you better be saying “Dear editors: I am just wishing to confirm that you received my story “Snarkdoms Gate”. If it did not reach you, please let me know so that I may re-submit it.”
5. Decide if you want to deal with them. I followed step 4 twice for a publication. I finally sent a withdrawal notice (“Dear editors: I regret to inform you that I withdraw my submission of the story “Snarkdoms Gate”. I hope to work with your magazine in the future.”), and had them beg me to send the story again. I sent it again, and still hadn’t heard from them four months later. I since withdrew it and moved on.
To keep track of your submissions you can use an online service, something simple as a spreadsheet, your own database, or a dedicated software program. I use a freeware program (runs on NET or Mono) called Sonar3.
Honestly, I only recommend taking a day a week for reviewing submissions and re-sending anything that’s come back. The rest of the time, write, write, WRITE.