Here are the formats we've done in the past, and their current status. I understand that there can be some confusion:
Format Status .nsr Deprecated. Will disappear in the next major release .nbe Supported, but not recommended. Will continue to be supported in the future. .xml (v1) Back in the Nessus 1.x days. Deprecated, will disappear in the next major release .xml (v2) Sometimes referred to as "xml-ng", was introduced in Nessus 2.x. This format is deprecated and will disappear in the next major release .xml (for windows) Nessus 3.0 for Windows had its own report format for a while .nessus (this is XML internally). Introduced in Nessus 3.2, this is the reference format for the future.
The .nessus file is documented here and is the format we fully intend to push in the future. Provided you use an XML parser to process it (and not just regular expressions) and therefore if you add the flexibility of ignoring unknown tags, the future extensions to this format will be backward compatible.
The big advantage of the .nessus file format is that it contains the full context of the scan -- the list of the targets, the actual policy used, the plugin set used, etc...
Bottom line: .NBE and .nessus are the formats you can/should use. (Note that it's fairly easy to convert .nbe to .nsr if you need this).