I much prefer footnotes myself, where you can see directly what is being cited. Unfortunately there's a wide range of practices for online writing, but the norm I've found is usually just hyperlinks to digitized sources.

The Appendix, the online history journal I helped create back in the day, tried to experiment with a more detailed way of doing in-line citations, via small icons that you can click to see images, citations of primary source texts, even music or films on occasion. You can see it in action here:

http://theappendix.net/issues/2013/10/made-in-taiwan-an-eigh...