Special effects — often abbreviated SFX — are, in terms of the BBC Wales production of Doctor Who, "special" practical effects. They involve the efforts of technicians dedicated to achieving an effect "in camera" during principal photography. At least in terms of 21st century Doctor Who, they should not be confused with visual effects, which are achieved in post-production.
Historically, there was little distinction between the terms "visual effect" and "special effect". People credited under the title "Visual Effects" during most of the 1963 run of Doctor Who often dealt with effects generated in-camera on the day of recording. Indeed, many major films, such as those in the original Star Wars trilogy, made no real distinction between "special" and "visual" effects, leading to a general public belief, reinforced by behind-the-scenes documentaries (and even magazine titles like SFX), that special effects has to do with CGI, green screen, and general post-production wizardry.
This led to the confusing situation of "visual effects" meaning two rather different things in the history of Doctor Who. In the original run, it definitely meant "special effects" until around the time of Time and the Rani. At that point, it became possible to have rudimentary visual effects achieved in post-production. (DOC: 7D FX) Even so, people credited under "Visual Effects" were still doing what would be called practical "special effects", in addition to what the BBC Wales production would call "visual effects", until Survival.