Autoptimize 1.6.5 got just pushed out, with one new feature and one notification. The new option configures Autoptimize to output the aggregated JavaScript in the head-section instead of at the bottom of the HTML. This can be useful when some of the JavaScript needs to be loaded asap and might prove useful to make jQuery plugins behave.
The notification might be less welcome for some users; YUI compression and the CDN options are marked as deprecated in this release. YUI compression was pretty exotic and required the installation of JAVA and the YUI compression jar, so I doubt anyone was actually using this. CDN options are deprecated as well; some people reported issue that I could not reproduce or fix. As I consider CDN not to be core functionality and as it can better be accomplished using e.g. WP Super Cache (which is a must-have companion of Autoptimize anyhow), CDN will indeed also be removed from Autoptimize. Expect the deprecated parts to be removed in 1.7.0 (which isn’t planned yet).