Hints for Computer System Design, Butler Lampson. https://www.microsoft.com/en-us/research/wp-content/uploads/...
End-to-End Arguments in System Design, http://web.mit.edu/Saltzer/www/publications/endtoend/endtoen...
I think Rich Hickey (of Clojure) makes lovely points about application system design. I know you are looking for papers, but Rich's talks have influenced me greatly of late. https://github.com/tallesl/Rich-Hickey-fanclub
I really like 'Hints for Computer System Design', Butler Lampson . He passes on useful experience without demanding much in preparation from the reader.
"Hints for Computer System Design" by Butler Lampson
Tough question. I'm not aware of any books that are substitutes for reading and writing large projects, some books I've found useful: TCP/IP Illustrated: The Implementation (goes through the implementation of the 4.4BSD-Lite network stack), Lion's Commentary on UNIX (or xv6 book), Network Algorithmics (amazing book), Linux Kernel Development by Love, Large Scale C++ Software Design, Design Patterns. A lot of people like the Architecture of Open Source Applications books. I also think learning more computer architecture as the beginning of computer systems engineering is good for everyone, but that's just me.
Lampson's classic on hints for computer system design:
Here is a previous HN post on the subject: https://news.ycombinator.com/item?id=8000811
The Clean Code author has a Clean Architecture book but I don't think it is out yet.
I'm less of a PARC fan and more of a Lampson fan. In fact, I'm a huge Butler Lampson fan. I've read his PARC valedictory Hints on Computer System Design many times and he's updated it recently. He went from PARC to DEC SRC (maybe 5 miles). I saw him give a talk at SRC and for about 15 minutes afterwards, I understood.
Hints is the favorite paper of a lot of my heroes like John Regehr.
From SRC, he went to Microsoft and he also taught at MIT.