Where BC (before Christ) follows the year, AD (anno Domini) precedes it: 100 BC and AD 100. The newer terms, BCE (before the common era) and CE (common era), both follow the year: 100 BCE and 100 CE. All four abbreviations are traditionally written in small caps, with or without periods (e.g., 100 b.c., 100 bce), but modern style tends to prefer full caps and no periods, as shown in the first two sentences of this article. Use whichever rendition your style guide dictates.
The first two terms have been used for centuries, appear in most print sources pre-2000, and continue to remain more popular in print than their newer alternatives, which seek to remove the sectarian connotation of the original terms in lieu of more traditional Jewish designations. While I dislike that the newer terms are easier to confuse on a quick glance and still rely on the Christian calendar despite doing away with explicit Christian language, they are here to stay. Do not assume that the newer terms only serve as hollow attempts at political correctness—while a few writers may use BCE and CE to only signal their moral virtues, these writers are much rarer than some pundits may have you think.
Neither set of abbreviations is lesser than the other; both are standard, acceptable, and used in professional writing. Use whichever you prefer—and do so consistently—unless your publisher or style guide dictates otherwise.