White Birch is a fine choice for a bookshelf. However, Birch is one of those woods that doesn't take stain very evenly. A simple shelf bought wood conditioner will not do a very good job IMHO to help get an even looking stain job. For a pre conditioner, I would use two or three light coats of dewaxed shellac cut 50/50 with denatured alcohol. I've found this to work quite well on woods that tend to be "splotchy" when stained (Pine, Poplar, Maple and Birch in particular).
Now to the stain.... Like I mentioned above, Birch tends to take stain very un-evenly (although preconditioning the wood helps tremendously). So a penetrating pigmented stain (which relys on pigment being trapped in the pores of the wood to color it) will work fairly well to highlight the grain, but NOT work very well to stain something like Birch or Maple dark. Oil based or water based won't matter. They will be about the same.
What you need for your project is to use a DYE
stain. Note, some pigmented stains use a little dye in the darker colors, but for a truly uniform "even" look, a pure dye stain would be the way to go IMHO. I like using the TRANSTINT dyes that I get from my local Rockler woodworking store. Here is some great info on how to use them:
Or.... a ready made dye stain from General Finishes (I really like General Finishes products they are much higher in quality than typical big box store type products IMHO)....
Or, if you can find one that suits your color requirements, a gel stain will also work quite well on woods that tend to be splotchy. A gel stain stays more on the surface of the wood so you can get a more even color consistancy when using them. However, like a dye stain, you will cover up the grain of the wood when using them. Particularly if staining quite dark. Gel stains (like anything else really) vary radically as to quality. I highly recommend the gel stains from General finishes:
However, they don't have anything that is near "black" in color. So you might want to ask at your local Rocklar or Woodcraft woodworking store if they can tint them darker for you.
In any case, test, test and test some more on scrap before you start. Keep a finishing schedule on each (so that it can be repeatable) until you get the results you want BEFORE you start your main project.