As the above seems to susggest, custom can mean very high quality, but the reality is that the term custom means nothing about the quality of the design or construction. It merely means that it was not production. Custom boats generally are built by the wealthiest sailors who can afford to indulge in their whim of the moment and by the poorest of sailors who feel that they can coble together thier dream for less money than a used production boat. They are designed by some of the top designers of all time or by some guy who has some design idea and either couldn't find or refuses to pay for plans to pursue that design. Some of the most beautiful yachts I have seen or sailed were custom, some of the worst pieces of junk were also custom.
It is a mistake to rely on either the builder or the designer as a source of build quality or sailing ability. Owners will often ask for a boat that is unusual for a particular designer and ask for a build quality, above or below the norm for that designer or boat builder.
Used they are not necessarily cheaper than equal quality production boats, but most times they are a little cheaper, because the buyer is being asked to take a leap of faith with regard to build quality.