Which ones? Awk is one; in fact Awk was almost co-developed with yacc. But it gives generally bad error messages. (There are multiple implementations, but most of them use a yacc-style LR(1) grammar and give bad error messages.)
I don't know of any others. Certainly ANTLR generates bad C/C++ code, so I would be very surprised if it's used in anything in a typical Unix/Linux terminal.
I have been blogging about Unix and parsing here, after writing a very complete bash parser by hand: http://www.oilshell.org/blog/
My conclusion is also that generic parser generators are not good enough for production quality parsers. This is borne out by evidence in the wild.
In other words, "real" languages don't use parser generators. Look at the top 10 languages, as well as emerging languages. Which one of them use parser generators?
Clang, GCC, v8, PHP, C# / Roslyn, Go, Perl, TypeScript, Dart, etc. all use hand-written parsers. Not sure about Rust and Swift, but I think they are hand-written. Java is an exception, but interestingly it has a "real" grammar, and then a LALR(1) optimized for parser generators:
http://trevorjim.com/is-java-context-free/
Python uses ITS OWN parser generator, not a generic one, which is a very important distinction.
I'm not sure about Ruby, I think it might be a yacc core with A LOT of ad-hoc parsing, so it may not count. Just like bash uses yacc for about 1/4 of the language, and ad hoc hand-written parsers for the other 3/4.
Anyway, I don't think parser generators are as widely used as you think, but I would be happy to be corrected.