The simple answer to make sure you don't feel ripped off, is keep going back to Chile. I do. My "reciprocity fee" was $61 just over 3 years ago, and I've entered 8 times :)

Peek underneath the receipt and there is a stamp. If you lose the stapled-on receipt, you are still OK. I know as I have reentered Chile numerous times without it (fell off and lost nearly two years ago in Peru) and was only once questioned about it by a male Immigration officer on a power trip/had nothing better to do as the lines were empty.

Like Eastbay1K, I've gotten my money's worth out of my reciprocity fee receipt. The one in my old passport cost me $20 in 1995, and counting up the stamps in that passport, I see I entered 25 times with it.

En estricto rigor, the receipt is good for the life of your passport, but if you're lucky, it can be good for longer than that. The first time I entered Chile after I had renewed my passport, I expected to have to pay the reciprocity fee (which had since risen to $100), since the $20 receipt now had holes punched through it like the rest of the old passport. But after some consultation between the fee booth person and the passport control people, I was given a new receipt without my having to pay.

A few months later I got my permanent residency card, and sometime soon thereafter, either on leaving or reentering Chile, someone in passport control removed the $100 receipt from my passport.

In the new passport, by the way, 14 entries so far, and counting.

Is it a valid assumption that this generosity was the result of having your permanent residency paperwork already in the system and being processed?

Actually, when I was last there, I am pretty sure they wanted a $45 reciprocity fee from UK passport holders.

Of course, I do know some people who don't see the UK as a European country. :p

They also charged Australian, Canadian and Mexican passports varying fees.

No, I don't think so. They didn't consult their computers before deciding I didn't have to pay the fee again, and I didn't mention having a permanent residency application in the works.

I didn't ask or do anything to get out of paying the fee; in fact, I did get in line at the booth and paid it, but then when I got to the immigration desk and showed the new passport along with the old one, the guy there said I didn't have to pay it, and walked me back to the booth and told them to give me my $100 back.

As I said, it could have been just my luck that day.

Do you have to pay the $100 visa fee if you are flying to Mendoza with a connection through SCL?

No need to pay as you can manage to stay airside.

I tried to go through immigration without it in March and was politely requested to pay at the booth :(

limo,
Did you have a connecting flight out of the country when you were required to pay?

No - I've done exactly this, and you can avoid Chilean immigration altogether. As you're exiting the plane in SCL, there will be signs and people directing if you're making a connection to Argentina.

Or, in fact, a connection to any other international destination ;)