I'm developing an open-source CMS called cms -db. (The current "stable" version is only available in German, but the testing version can be tested in English at http://staging.cms-db.de/)
One reason for using WYMeditor in my CMS is that I think valid and semantic correct markup is very important. An other reason is that TinyMCE which I was using before is very big (WYMeditor reduzed the size of the archive by over 200 KiB) and has too many features (which is confusing to new users). And I really like how easy it is to extend WYmeditor just by looking at the examples.
I had only one real problem with WYMeditor until now which is preventing me from implementing an auto-save function. (see bug #147)