PHost 4.x is the current major release. Some often-requested features, most notable support for 999 ships, required a departure from old file formats to new ones, and we used that opportunity to add several all-new features as well. After almost four years of beta status, version 4.1 marks the point where we think the 4.x series has reached production quality.
PHost 3.5 is part of the old "mainstream" release of PHost, the successor of PHost 3.4, 3.3 and 3.2. As the version numbers show, they are all compatible, as far as file formats are concerned. We provide version 3.5 to support existing games. Since the 4.x series now has reached production quality, we'll slowly phasing out support for version 3.x.
Up to now, every 4.0 release has been accompanied with an "almost equivalent" 3.4 release, where the 3.4 contains all the bugfixes and some of the new features of the 4.0 version. In the future, this relationship will be loosened; version 3.5 will receive mostly fixes only.