I think that BCE/CE should become common practice. We are aiming for a scholarly encyclopedia, and that seems to be current scholarly practice.
Anyway, if I were writing "AD" - Anno Domini - it would be in the year of our Lord - I would be presuming that the reader is a Christian, or maybe the reader would presume that the writer is a Christian. What if my 'Lord' is someone quite different from Jesus Christ? It may be "in the year of our Lord, Immanuel Kant" - in which case, the dating would be off by quite a significant amount.
Also, the Common Era is actually different from the purported life of Christ - the evidence suggests that Jesus was born after year zero, instead - according to Wikipedia - in 7-2 BCE. If you use 'BC' terminology, then Jesus Christ was born before Jesus Christ. Sorry? That doesn't make sense. Use Common Era terminology and that problem goes away.
See
http://www.google.com/search?q=common+era+site%3A.edu for instances of 'Common Era' on .edu sites
Similarly, many standards efforts that have worked on date formats for computers specify 'Common Era' phrasing.