Version 3.0 of the fbcwp plugin is a fairly substantial update, partially because facebook themselves have released version 2 (v2) of their comment system.
In light of this, I'm going to provide a brief rundown of what's changed, and some useful info.
= New options =
* You can now be notified via facebook notifications of any comments (multiple user IDs can be specified in the settings page).
* You can switch between v1 and v2 on the settings page of this plugin. By default, v1 is used since v2 is somewhat buggy / lacks features that are in v1.
Note: While using v1, threaded replies likely won't show. Also, facebook seems to be constantly updating v2, and sometimes some comments disappear. Though, they've always come back on my test site.
* You can enable both v1 and v2 at the same time, though I don't recommend it. But, it's there in the settings for anyone who wants to. Also note that this setting uses both the page/post url (v2 method) and xid, whereas using just v2 fetches via the transitional 'migrate' flag.
Here is a brief summary of what changed in facebook's v2 of their comment system. These changes were made by facebook and so can't be undone (you can still use v1 though) see here for more.
* No more built in like button
* No more custom CSS: "We want to make the Comments plugin consistent with the others, so we will most likely have a dark styled version, ability to specify font, etc., but unfortunately, not have custom css." - Cat Lee, Program Manager, Developer Relations at Facebook
* No anonymous comments, but can login with other sites (currently Yahoo!, but they say more are to come). Note that anon comments don't really work right in v1 either (see: http://bugs.developers.facebook.net/show_bug.cgi?id=14126).
* No more sorting chronologically. v2 uses a system somewhat like digg's, where the comments it thinks are best are displayed first.
* Comments made in v2--on posts which have no comments from v1--won't show up on the dashboard, the recent comments widgets nor will they be included in a post's comment count. This is because the method by which this data is retrieved (FQL) is currently returning empty queries when using the new v2 query. Note that if a post has comments on it before switching, everything will report correctly for that post.
= v2 issues/bugs =
* can't reply to v1 comments. This seems to be a facebook bug
* replies are sometimes also displayed as single, unnested posts if the page is refreshed (see: http://bugs.developers.facebook.net/show_bug.cgi?id=15583)
* currently no "dark" options to style the comments. facebook devs say it's coming soon
* posting using alternate facebook identity not working
I'll be keeping up with v2 dev and updating this plugin as necessary to accommodate any changes they make. I expect facebook will fix the v2 FQL soon, since it's the only way to get comments from the new system, and many people have complained. Once that's fixed, I'll update the plugin so it displays/counts comments on the dashboard and in widgets for posts with only v2 comments.
If you find any bugs/issues, please either post them here, email them to me or add them here: https://github.com/shaund/Facebook-Comments-for-WordPress/issues
Updates coming in the near future
* Option to automatically include like button with v2 (only reason it wasn't in this version was because I want to be sure there are no conflicts)
* Storing facebook comments in the WordPress database