intellij-idea allows customizable stack trace folding, especially useful with dynamic languages.
(source: jetbrains.com)
and an Analyzing external stack traces tool.
I can imagine general tool/filter working on logging framework (like logback or log4j) level. I don’t think there is any general support for that, but I think it is a great idea to implement this. I will have a look, maybe it is not that much work.
UPDATE: I implemented filtering irrelevant stack trace lines in logs for logback, also follow LBCLASSIC-325.