As Bethberry posted in another thread, Letters by Tolkien is getting a facelift and will be published soon. There are various books of Tolkien artwork which often contain analysis and comments, as well as The Road Goes Ever On, which contains a few of Tolkien's songs or poems, set to music with JRRT's approval. There are various publications that produce snippets of Tolkien's writings that are primarily linguistic or philosophical in nature but do contain nuggets. These include Parma Eldalamberon and Vinya Tengwar. There is a journal of Tolkien Studies that is primarily analytical or scholarly, but sometimes includes papers that discuss and analyze materials in the Tolkien collections of Marquette and the Bodleian (which do contain drafts that include alternative wording or versions, often rejected). One of our members, William Cloud Hicklin, recently published Chronology of the Lord of the Rings (discussed here
http://forum.barrowdowns.com/showthread.php?t=19520) based upon Tolkien's own notes. Hammond and Scull have published the Tolkien Companion and Guide, and an LoTR Reader's Guide which contain snippets of some unpublished materials. So there exist unpublished materials, mostly of interest to scholars and the obsessed (no insult to anyone intended, one man's dross is another's treasure), that find their way into the world through various vehicles.
However, if you are asking whether there are substantial unpublished Middle-Earth writings and stories that are more or less completed (as opposed to fragments, notes and memos), the answer is likely no. Most of the substantial drafts by JRRT were published in HoME.