Probably the four most well-known pieces of software with end-to-end verification of functional correctness are the CertiKOS microkernel from Yale (verified in Coq), the SEL4 microkernel (verified in Isabelle), the Compcert C compiler (verified in Coq), the CakeML ML compiler (verified in Isabelle).
Stopping short of full end-to-end functional correctness, there are lot more notable examples, such as the Verve system at MSR (verified type/memory safety using Boogie), and the Bedrock system at MIT (functional correctness down to a fairly low-level IR, done in Coq), the miTLS/Everest TLS stack (protocol correctness verified in F-star, most of the way down to a C-like implementation), and the Iris project (a toolkit for verifying higher-order concurrent programs, currently being used to formalize Rust including unsafe, in Coq).
In machine-checked proof, the three biggest successes are the verification of the Odd Order Theorem (in Coq), the Four Colour Theorem (in Coq), and the Flyspeck project verifying the proof of the Kepler conjecture (in HOL).
In hardware verification, there has been a huge amount of work using ACL2 and HOL, but I don't know this space as well.
Basically, Coq and Isabelle have the most actual successes, but other things like F-star, Boogie and HOL have all worked as well.
Stopping short of full end-to-end functional correctness, there are lot more notable examples, such as the Verve system at MSR (verified type/memory safety using Boogie), and the Bedrock system at MIT (functional correctness down to a fairly low-level IR, done in Coq), the miTLS/Everest TLS stack (protocol correctness verified in F-star, most of the way down to a C-like implementation), and the Iris project (a toolkit for verifying higher-order concurrent programs, currently being used to formalize Rust including unsafe, in Coq).
In machine-checked proof, the three biggest successes are the verification of the Odd Order Theorem (in Coq), the Four Colour Theorem (in Coq), and the Flyspeck project verifying the proof of the Kepler conjecture (in HOL).
In hardware verification, there has been a huge amount of work using ACL2 and HOL, but I don't know this space as well.
Basically, Coq and Isabelle have the most actual successes, but other things like F-star, Boogie and HOL have all worked as well.