Well, it is a big topic, but in brief:
Traditionally, suttas have been referenced by describing their position within a collection. Eg. “the seventh sutta of the sixth vagga of the second pannasa of the Majjhima Nikaya.” This is useful, because it applies across manuscripts and editions. Imagine looking for a sutta among a pile of manuscripts; this descriptive approach lets you successively narrow down your search to find what you need. The disadvantage of this system is, of course, that it is verbose and complex.
Following the publication of the PTS editions, it became conventional in academic work to reference them, usually by volume and page. This is convenient for someone who has these editions, but it breaks from tradition by tying the reference to a specific printed edition. In retrospect, it was a mistake that the PTS did not introduce a more sensible system. (They did in some cases, eg. the Vinaya and Digha Nikaya, but these are rarely actually used.)
Modern digital editions, and Asian editions generally, use their own systems. Probably the most widespread digital text is the VRI edition of the Burmese Sixth Council edition. SuttaCentral uses an improved version of this, known as the Mahasangiti edition, but the numbering is the same.
Meanwhile, in EBT circles, it is more common to reference suttas by their number. that way you avoid the verbosity of the traditional system, and the edition-specific limits of the PTS system. This is the normal system used by Ven Bodhi and Access to Insight, to name two influential sources.
For our texts we adopt this semantic numbering system, standardizing to the numbers as used by ven Bodhi, in the few instances where this differs from the Mahasangiti. Thus as a general rule you will find we use the same numbers as Ven Bodhi, and also Access to Insight.
In addition, we are in the process of segmenting the Pali texts so that they may be referred to by a more granular system. This is compatible with the normal semantic system, but adds the ability to reference much more precisely. Eventually, this will result in a “chapter and verse” reference similar to that used universally for the Bible. Currently this system is working for the four nikayas, and I am preparing the Vinaya texts.
In an ideal world, i would hope that people would standardize to this system, which is vastly preferable to any other. But, as you may have noticed, we do not live in an ideal world, so I expect that people will still keep using different systems.