They come in different formats. If you download an e-reader app (i used to use Aldiko) you can drag and drop any ebook file onto your nexus and read it. Amazon uses .mobi i think, so if you have a load of those, you can put them on your Nexus and read them fine. Or, you can download the Kindle app and just sync your library straight away.
I'm not sure what Google Play uses, or how they allow you to move the files around. They might use .epub, which Aldiko can read, but a Kindle can't...
Basically it depends on how flexible you want to be. If you're just planning on using one store or another, then just use that and stick with it.
That was even less helpful than my previous post i think. Sorry.