this is maybe too broad a question to get a useful list, but i'll take it at face value:

Hanging Temple near Datong, China

Thanks midlander! I'm keeping it very broad on purpose, just to see what comes back. 

I'm hoping for buildings with a sort of special effect/feeling of transition between inside and outside.

http://www.archdaily.com/554132/ad-classics-yokohama-international-passenger-terminal-foreign-office-architects-foa/

Think Salk Institute qualifies.....

machu pichu 

mesa verde

greek theater near temple of Apollo.  

too many to list...

Have a look at R.M. Schindler and Richard Neutra. 

Interesting how a lot of the 'buildings' listed so far are either ancient and/or could just as easily qualify as 'places' or  communities. Could it be because so many marvels of modern architecture tend to be object buildings? I feel like many iconic contemporary buildings tend to reside on a plinth of sorts--elevated above and detached from the site, landscape. 

I also would note that there's a difference between the building working tectonically with the site, landscape and simply exalting it , such as the Salk institute. 

good point Larchitect.  there are so many Ironies in that.  as art has become more "field" based...as our understanding of the "axis mundi" has been completely flipped by modern physics and astronomy...our buildings seemingly act more as if they sit at the center of the universe...

its almost as if architects are narcissistic or something...but we know that cant be true...lol

Detachment seems to explain alot of our modern ills. 

Thank you Larchitect and jla-x...you have hit the nail on the head. I think detachment is the right word for this syndrome.

Here are some of my tops to get the ball rolling again! (Modern selections)

Muuratsalo- Alvar Aalto

Casa Malaparte- Adalberto Libera

Luis Barragan - so many things

RM Schindler - Kings Road House

Carlo Scarpa - Brion Vega Cemetery

Enric Miralles and Carme Pinos - Igualada Cemetery

All buildings have a significant relationship with their site, intentional or not.

I recommend the book: Site Matters edited by Carol Burns and Andrea Kahn. 

I find complex, often antagonistic relationships with site just as interesting.