The gemara says that R' Yochanan would sit at the exit to the women's mikveh so that all the children would be like him. Rashi explains that R'Yochanan was very handsome.
This gemara is also in Bava Metziah, and there the gemarah says that the children would learn Torah like R'Yochanan. The Meharsho in Bava Metziah explains that the "machshavah beshas zivug" determines what kind of person the child is.
1. Why would the first thing someone sees coming out of the mikveh or what she's thinking beshas zivug determine the nature of the child?
2. Why Rashi would not say the purpose of children being like R'Yochanan was so they would learn Torah? Is outside beauty that important? Doesn't the pasuk say "sheker hachein vehevel hayofi?

Such is the power of thought. This is true not only for humans, but for animals as well. This is what occured when Ya'akov avinu placed the marked rods at the feeding troughs of the sheep so that they would produce offspring with similar markings.

If you're looking for a scientific (non-metaphysical) explanation for the mechanism through which this phenomenon works, good luck....

That's only half the passuk. It's a contrast. Without "yirash hashem" then those are sheker and hevel. But is the absolute worldview of Torah that physical beauty is sheker and hevel? Certainly not. In many places the physical beauty of people are pointed out. It's only false and empty if the person is false and empty.

Maybe.
Another pshat in Rashi:
The fact that R'Yochanan was handsome is what brings about the heichi timtze of the maharsho, vehamevin yavin.

That seems strange. Its sort of like saying that the women should notice how handsome R. Yochannan was before they went home to their husband so they could have him in mind.

Yes, it is strange.

This story is the basis a custom that we have today, whereby the mikvah lady says some kind words to a women when she emerges from the mikvah.

In line with what Payel is saying. The fact is we dont want the woman to see an impure thing when she comes out of the mikvah. It has a hashpa'ah. So we try to arrange for her to see someone who is not "Tumeidik". The same with R' Yochanan. Its not that he wanted the women to be thinking of him pre se, but to have the impression of a Kadosh V'tahor on the woman,and its positive effects it has on the subconious. Which subsequently positively effected the concieved.

I think this is the reason pregnant women aren't supposed to go to a zoo. We don't want their thoughts to focus on animals, causing for them to possibly take the form of an animal.

I think there's even a bigger question about R' Yochonan. The hagaot habach explains that the reason the gemara didn't ask about R' Yochonan's yetzer hara, but it did by R' Gidel was because R' Yochanan had very long eyelashes that completley blocked his vision.

How is that beautiful?

I dont think its the form we're afraid of as much as the hashpa'ah of what they represent and how those midos can affect the vlad.

You are correct, that's what I meant.

He was also HUGE!
The beauty refered to here is probably the glow and hadras panim of someone so kadosh and Tahor. Not necessarily the superficial physical beauty we think of.
Although, Reish Lakish was attracted to him on that superficial physical level. Maybe the kedushah influenced the physical attraction. Maybe fat men with long eyelashes were all the rage back then! Questons ! Questions!

Where do we see that he was fat?

I forget the exact source. But the Gemorah describes his and Rav Hunah's girth.When the two stood belly to belly a herd of cattle could pass beneath them.

That gemara is not about R' Yochanan. It is in B. Metzia 84a. The Gemara about R'Yochanan's girth? We learned it a week ago. He was allowed to lie on his back, since he was a Ba'al Bosor.

Um....not counting National Enquirer articles, has this ever actually happened?

You are correct. The subsequent gemorah discusses R' Yochanan's and Rav Papa's girth. Which would explain my confusion.

Yes and know. See the discussions [in Niddah or YD HIlkhos Niddah] about a woman who miscarries a feotus that has animal form [as is to be expected in a foetus]. Also see the teshuvos about [not] killing a baby that was born deformed, resembling an animal. What eklse could have caused these phenomena?