Has anyone else noticed that in most animes there seems to be three goddesses or preistesses?
The number three is an important number. When things are in threes people see them as balanced. You can have 2 extremes and one that is kind of in the middle.
The number 3 is important in religion as well. (The most obvious here is Christianity-- there are also three major vehicles of Buddhism etc).
On the more technical side, triangles are facinating shapes. So many mathematical problems can be solved using triangles.
Not to mention things that appear in art such as trifoils.
The number three is a sort of standard. And, as you can see, it works (and you KNOW people go with what works). The chemistry you get from the 3 different personalities in the various animes you mentioned are what make those characters so attractive. By themselves they probably wouldn't be as appealing. But when they come together comic mischief ensues!
Certain other number combinations work as well... but I myself am facinated by sets of three...
Other notable Anime Related 3's
The goddesses in The Legend of Zelda as well as the Triforce.
Rockman, Forte, and Blues form a sort of set of three (good, evil and mysterious). The same can be said of the X series between X- good, Zero- mysterious, and Sigma- evil.
Pita Ten - Misha is an angel, Shia is a demon and Kotaro is the human in the middle (the main one anyhow).
In Final Fantasy games, you traditionally have 3 members in your party (not in Final Fantasy 1 though -- you had 4).
Gundam Wing starts out with three major political groups, The Earth's Sphere Alliance, OZ and the colonies... which then divide into about 7 different factions by the end of the series O_O
You get the idea... 3 is good...