I maintain a PDF rendering plugin that has this architecture:
browser side of the plugin (npshell.c) -> external helper application
The external helper application uses GTK 2.x and Poppler to do the job and embeds itself into the browser window using XEMBED and the window ID supplied to via GtkPlug. The problem is that although the initial contents of the window appear, i.e. the first Expose event arrives, subsequent events are not received by the helper application: mouse clicks / motion detection don't work and Expose events (apart from the first one) don't arrive either, so resizing the browser window messes up the plugin area. E.g. the plugin is able to rearrange its widgets according to the window width and uses the Expose event to detect the new window size. But it doesn't even happen.
The plugin exhibits the above described problem in WebKitGtk-base browsers, like Epiphany and a custom little application using the WebKitWebView widget. Both Epiphany and the custom browser app were tested under Fedora 17 (webkitgtk-1.8.3) and Fedora 18 pre-beta (webkitgtk-1.10.0)
The plugin works flawlessly under Firefox and Chrome.
Support for plugins was removed in https://trac.webkit.org/changeset/265753/webkit.