Both types of microphones are well versed for conference room applications. Many variations of both types are available to accommodate the specific needs of the customer. Over the last 10 years we have definitely seen a trend calling for a lower profile microphone on the boardroom table.
Boundary layer microphones certainly meet the criteria for today’s conference room. Small and inconspicuous, they are usually placed 15 to 36 inches (400 to 915mm) away from the participant. Because the microphone element is in such close proximity to the table surface, phase cancellation problems are virtually eliminated. This is the result of direct and reflected sound reaching the capsule almost simultaneously. Some boundary layers even have multiple elements. This scenario not only minimizes the number of microphones on the conference table, but also involves less labor, without sacrificing audio performance.
Gooseneck microphones are still very popular in boardrooms. Offered in different patterns, lengths and sizes, they are often selected when gain before feedback is a major issue. Because of their reach, they can bring the microphone capsule much closer to the source and therefore increase the intelligibility in difficult situations. Another good example would be lap top computers. If you open a laptop and block the boundary layer microphone, there goes most of your pick up. A gooseneck microphone with a longer shaft length would probably be more appropriate in this situation.
The bottom line is that both microphones are very good choices. Final decision should be based on the particular application, the environment, the end user requirements and also aesthetics.