Although I use most of the housing controls at one time or another, I think which controls you use the most often depends on your shooting style and whether or not you use TTL strobes. I do use TTL strobes for every strobe shot I take, wide-angle or macro, and feel it increases the number of one shot opportunities I get right. I also use auto-focus lenses on auto-focus much more often than I use manual focus, which I do like for some situations.
Given those parameters, the controls I use, in their frequency of use is as follows: (1) the trigger - both to take the picture and to initiate auto-focus. (2) the zoom control to vary what the lens is seeing. (3) the flash compensation button - to vary the strength of the flash depending on what the picture needs. (4) the aperture control knob - usually to vary aperture of the lens to provide the overall exposure to work with the ambient light and to control depth-of-field. Sometimes, when I shoot in shutter priority auto-exposure, this knob can be used to vary the overall exposure compensation. (See the Nikon custom function called "Easy Comp) (5) the shutter speed control - to vary the overall exposure and and to stop or blur subject movement. On many dives this just stays somewhere between 1/125 and 1250 for the whole dive. (6) the M-S-C control which I sometimes use to switch to actual manual focusing but more often use as a focus lock for repeated shots at the same distance. (7) The manual focus control for the lens, especially used with wide-angle lenses (8) the Function Button (on my D700) which I have programmed to turn off the flashes. This is much easier than trying to reach up to each strobe to turn it off or on. Sometimes I turn the flashes off for an intentional ambient light only shot. At other times to check ambient light metering before I add fill flash. (9) the ISO button. With the D700 I usually shoot at ISO 400 or 800 the whole dive. (10) the Focus Lock button (programmable on my D700) which I usually have set to utilize a Nikon function called Flash Value Lock. If you are a Nikon user and haven't looked into this capability I think you're missing out on a really good function. (11) The housing latches to open the housing at the end of the day to download shots and to change the camera battery.
Fred