As a BGO, I've seen this question many times. First of all, this issue primarily concerns MOC noms as the SAs don't care if you apply to more than one and your chances at one will not be harmed by applying to more than one. It also does not apply to USCGA, which does not require noms.
There is no definitive answer. However, here is some guidance. IF you live in a competitive geographic area (examples include: VA, MD, PA, TX, CA, FL and numerous others) where there are many more candidates than available nomination slots, my recommendation is that you choose up front the SA you most want to attend and put all your eggs in that basket.
The reason is that MOCs will typically ask you to pick one SA or at least rank them (most require you to pick). If you pick one SA for two MOCs and one for your third MOC, you risk not getting an interview for the "one" MOC. This happened to one of my candidates. He listed USMA first with two MOCs and USNA first with one. He didn't even get an interview from his USNA MOC so his choice was made (he did get into USMA, so all not lost).
The above strategy (distributing your picks among MOCs) is perfectly "legal" and works IF (and only if) you would be equally satisifed at more than one SA because, in competitive areas, you are extremely unlikely to get a nom to more than one SA from the same MOC.
If you have a Pres nom, the above strategy may not be as dangerous because you know you have a nom to your school of choice. However, relyiing on a Pres nom alone is also dangerous -- although many people do get appointments with only Pres noms, many do not. Pres noms are not competitive and SAs like to see candidates earn competitive noms from MOCs. Not required, but desired.
IF you are in a non-competitive geographic area (for example: AK, ND, SD, MT, ID, WY), there may be more nom slots than there are qualified candidates, just based on population density. In those cases, you may be able to obtain noms to more than one SA from the same MOC.
The bottom line is that, at some point, you'll have to make your choice. My strong suggestion is to do all the research you can during your junior year and senior summer so that your decision is made by the time you must state your preferences to MOCs.
Two other points. As noted above, USCGA is a GREAT school and does not require noms, so always consider applying to it (I applied and was accepted and almost went there -- great school). Also, USMMA is a great option that is not as "popular" or well known. Thus, you may be able to "double up" a nom to USMMA plus one of the "big 3" SAs.
Good luck!