If you need better support for third party drivers or software then 9.3 would be the better choice. FreeBSD 9 has been, as you say, around for a while. In this respect 10 is a relative newcomer. As far as package management goes I do believe 9.3 also has the new package manager in the same way 10.0 has and 10.1 will have. The only difference being that 9.3 still contains the 'old' package tools, they've been removed in 10.x (although you can still build them if you wish). There are some interesting new additions and improvements in 10.x though. Have a look through both release notes, the important ones are all mentioned. Pick the version that matches your requirements.
Anyway, both versions, 9.3 and 10.1, are usable, up to date and have minimal bugs. There would be no point in releasing them if this wasn't the case. Updates and support will be available for the next two years for both version too.
