From 0.9.5 onward PCSX2 has been a mostly open SVN revisioning process, where beta builds are SVN-marked and are widely built and distributed to users. 0.9.5 itself was never released as an official 'stable' build, and after the release of 0.9.6 we just called all subsequent SVN builds of PCSX2 "betas." (mostly because we were too lazy and/or busy to bother worrying of version numbers). This lackadaisical version pattern was a source of confusion for users and developers alike.
So starting with our next release of PCSX2 we'll be using an established versioning pattern (which likely won't be for some time -- implementing a new GUI is a complicated ordeal). The new patter will be based on some standard Open Source convention, where odd-numbered versions denote SVN/devel builds (and will have SVN numbers affixed to the version) and even numbered versions denote stable releases. By chance this is already how things have been playing out since 0.9.5, so mostly it just means we're making a conscious effort to continue to apply the pattern in the future. Thus, the past-present-future will look something like this:
Past: 0.9.4 - Official stable release 0.9.5 - Development build (SVN)
Present: 0.9.6 - Official stable release 0.9.7 - Development build (SVN) [wx-enhanced!]
Future: 0.9.8 - Official stable release 0.9.9 - Development build (SVN) 1.0.0 - Official stable release 1.1.0 - Development build (SVN)
This way when people file bug reports we can know from the main version number alone if the report is regarding a stable release or an SVN build, and furthermore users can have a clearer guide to the status of versions being released and such. Furthermore, odd versions will have the SVN revision appended to them by default, like 0.9.7.r1880 .
... and yes the hope is that we're going to go to 1.0.0 after 0.9.9, and use a 1.0, 1.1, 1.2, 1.3, etc version pattern, shortening the primary version numbers from three digits to two. But that's a long way down the road yet, and anything could happen between now and then.