Following a Cook's Illustrated recipe, I started work on making vanilla bean extract last fall and just now got to bottling it today. Even though, per recipe, I could've strained and bottled it after only a week, the color of the extract had me worried because it wasn't near as dark as my store-bought one. I even reheated it and added an extra vanilla bean at one point. (That's when I took the above photo, and you can see how translucent the extract is in the jars in the background. The store-bought one I was using for comparison let almost no light shine through at all.) Letting it sit for a long time didn't do any harm, in fact you can leave the beans in indefinitely if you want, but it also never got all that much darker. It's in a brown glass jar here, but you can see that its still pretty translucent.
Turns out that didn't matter, but I'd still like to know how they got theirs so much darker than mine. The Mister and I did a taste test in plain milk today, homemade vs. store-bought, and both liked the homemade better. The store-bought flavor was overwhelmed by alcohol, whereas I could barely detect it in the homemade. Not sure why that would be—maybe the grain alcohol in the store-bought is higher proof than the vodka I used in mine? I went with organic vodka, by the way, which I was so happy to find even existed. Turns out there are actually a number of brands of it available. I chose one called "Rain" because it was the least expensive.