I always thought Apache 2 and Subversion were two of the best examples of second-system effect. I mentioned this once to one of the core Apache (and Svn) developers years ago, and not only was he blissfully unaware of the effect, he indicated that he had helped build incredibly successful pieces of software (ie., Apache 1.x) and didn't need any advice from from Fred Brooks or anyone on how to do it.
Both Apache 2 and svn have been extremely successful projects, but both were late, didn't really match expectations or even the success of their predecessors, and are slowly being outcompeted by much smaller and usually more efficient projects (eg., nginx, lighttpd, git, hg) that are developed much more quickly by much smaller teams.