In Europe usually you don't need to go through immigration to change planes (unless you are entering/exiting Schengen). Is it the case in the US as well? May I catch a connecting flight on one of the US airports if I don't have US visa?
Unlike many other countries, US airports do not have any form of physical immigration controls when you are departing the country on an international flight. In fact, in most airports there isn't even a concept of an "International" terminal/gate, with the same gates frequently being used for international flights and domestic flights.
As a result of this they can't enforce the concept of a 'transit' passenger - once you're in the departure area, even if you got there on the pretext of catching another international flight out of the country a few hours later, there's nothing to stop you boarding a different domestic flight, or even simply walking out of the airport!
This means that ALL passengers arriving on international flights in the US must have the legal right to enter the US; i.e, you must either be a US citizen/green card holder, be from a country that does not have any visa requirements (such as Canada or Bermuda), be from a country that is a part of the US Visa Waiver Program and have a valid ESTA, or have a US Visa.
If you require a Visa then there is a "Transit Visa" (C) available which is normally a little easier to obtain than a normal visa, but you'll still need to go through the full visa application process, including showing proof that you intend to leave the US (almost) immediately.
First of all it depends what nationality you are. I assume you are from a country that is part of the US visa waiver program. In this case you don't need a visa but you do need a travel authorization (ESTA) even if you are only changing planes in the US without leaving the airport.
Source: ESTA-FAQ of the Department of Homeland Security.
So there is no difference between visiting the US for 90 days or just transiting, in both cases you need an ESTA. It currently costs $14 and you can do it online before leaving for the US.