The good example is app-text/dgs, which was removed from the tree and needs to be restored again. As seen in http://bugs.gentoo.org/show_bug.cgi?id=98762#c46 this problem was introduced in automake 1.9.6. This is a blocker on unmasking modular X, because we need the pswrap utility from dgs. (Yes, we can hack up a workaround if this can't be fixed in a reasonable timeframe.)
i'm not sure it is a bug introduced by 1.9.6 ... just a long standing bug that was finally triggered with 1.9.6 ... ive posted a patch to the automake list and will get back to you ...
1.9.6-r2 includes a fix for this ... seems to work for me