At the most basic level is the application of oil to the unfinished marquetry to bring out the tone and highlights of the wood. The best oil for this is poppy oil. This is a clear oil used by artists. Rub a light coat briskly into the wood. Apply a wash coat of Shellac afterwards and then apply the top coat of your choice.
By far the most popular method for enhancing parquetry is "sandburning" or sand shading. In this the veneer is submerged into fine hot sand. It only takes a second to effect a change and a little practice goes a long way. In many instances, I believe, it is overused. A subtle effect is ideal as in the piece below of Mont Saint-Michel by Franck Debouverie.
Another ancient solution was the use of acid. This was usually nitric acid in its many forms and often diluted to useful levels that were less dangerous. Not used anymore except in antique restoration where new wood is treated to match the patina of old wood.
Pyrography and marquetry can be combined to produce spectacular results in the hands of a seasoned craftsman. The problem is that it can easily overshadow the marquetry to the point of obscuring it all together. As it is applied to the veneer after glue up, a heat resistant adhesive must be used. This method cannot be undone. It appears this method is underused.
Engraving has been around as long as sand shading and is little used except in restoration. It was heavily used to highlight tortoiseshell, brass and silver in centuries past. The knife is most often used today in this procedure after lines are drawn on the sealed marquetry. Black wax is rubbed into the cavity afterwards.
Finally there is penwork. This is the application of ink upon the marquetry to illuminate it with detail. A pen is used with a nib of the desired thickness. This is applied after the parquetry has been sealed and sanded. A level surface is required. Black India ink is best. Most ink contains alcohol to speed drying so a top coat of Shellac will result in bleeding. An oil based varnish is a better choice. Used mostly in Far East countries to enhance unanimated marquety as shown below.
Even among purists, there is an attitude that most of these techniques are unacceptable. In some juried competitions they are outright prohibited. The consensus is that the selection of veneer for its grain, tone and contrast should preeminently determine a persons ability as an artist. I agree, but it can be an asset to display a little form on an otherwise flat surface.