It is a subjective term use by vendors. It has no real wolrd meaning, such as "Reference Speakers by Vendor A are better than non reference models by Vendor B".
In general terms the vendor/designer would offer a Reference Line or Model that would possibly use better quality pieces in construction. This can be cabinet materials, finishes, a driver that meets very stringent test specifications and many other similar techniques. Suffice to say that if vendor A offered Model 123, and a Model 123 Reference, the Reference "probably" would contain better quality. I say probably because that is not always the case, and they don't always sound better.
Axiom offered a Reference Line of the older AX series. The difference was real wood veneer finishes (as opposed to vinyl), biamping/biwiring capabilities, and maybe a few other items.
Also, if an end user refers to their "reference piece", it refers to a piece (CD, turntable, speakers, particular musical selection) that they have heard and are accustomed to the sound. This is particularly useful for comparisons.
There are also companies that make use of the term in their names, such as Reference 3a Speaker Manufacturing. As a point of note, this company makes EXCELLENT speakers....some of the best ever to grace my listening room! They also are very pricey.
Hope that helps.