I use plain old Word docs, one for short stories, one each for novels.
I also have a handwritten list of what story is out where and when it was subbed, which hangs next to the computer. I have seven in circulation at the moment, so I tend to forget what's where and whether I need to nudge yet.
Spreadsheets work fine, too.
I've never cared for online tracking systems. I like my own idiosyncratic set-up. But the only thing that matters is that YOUR tracking system makes sense to you and keeps you on track.