Open Worldcat Advanced search gets 120 hits for the subject search: encyclopedias alternative. This will take a lot of sorting out, however, because many are "main-line" encyclopedias of alternative medicine, alternative energy sources, etc. Possibly you can find some by not limiting to subject or title, and searching something like: revolutionary encyclopedia (88 hits), or better yet, controversial encyclopedia* (81 hits). Limiting to subject, controversial encyclopedias, seems to be too restrictive, with only 13 hits. You can also try subjects that by their nature are controversial, and therefore might have encyclopedias done from a particular perspective; for example subjects such as: Occultism – Encyclopedias, Parapsychology – Encyclopedias, or Supernatural -- Encyclopedias. Atheism encyclopedia* gets 8 hits, limiting to subject cuts that to only 3.

Since the Web allows much cheaper publication, it is also well worth trying to find such encyclopedias there (unless of course this is for an assignment that requires finding print sources). The Google Directory gets a few possible leads, as does Yahoo Directory. Yahoo has an Issues and Causes category, and it’s worth searching: encyclopedia under some of those that seem interesting to you.