Along with having an organization system that allows you to see all of your polishes, another really helpful way to really know what you have is nail wheels.
They don't look exciting when they're new, but when used...
Every polish that I own is represented somewhere on these wheels. I've only been using these for a few months, but they've made a world of difference in how I choose which nail color to use. Instead of picking which color looks best in the bottle, I can hold up these swatches and see, not only which looks prettiest, but which is most flattering against my skin/clothes/etc, and I know exactly the shade it will be when it's dried (and there are some polishes that change a lot from how it looks in the bottle).
I have the brand and name of each polish marked on those little white stickers around the perimeter as well as how many coats it took to make the swatch. This helps because I have an idea going in about how many coats it will take to finish my nails with a particular polish.
I have mine grouped by brand since I already have an idea of how well different brands wear, but there are many other ways you could divide them (color family, finish, etc).
In addition to being able to see them all, just going through the process of painting all of them has made me extremely (almost painfully) aware of what I have. There are a few bottles that I don't think had been opened for years - I actually found some colors that are gorgeous that I wasn't really aware that I had. I also realized that there are certain types of shades that I have plenty of already, so I'm able to be much more discriminating about new polishes that I purchase.
I got mine from transdesign.com - $6.75 for a pack of 10 - a very small investment for how helpful they are.
You can also get then in opaque white, but I chose the clear ones because I think that the white ones could make it difficult to judge when light colors get good coverage (and mess up my number of coats system).
Even though I ordered mine, I'd imagine you could find something similar to these in any good nail supply store.
Thanks for reading.