Are there any kind of logs per user account, for eg: hours logged in, etc.
Or any kind of third party software's to analyze software usage patterns per user account on Windows Server 2008 R2
The logs exist, but they require 3rd party abstraction tools to get at. On individual workstations, if you analyze the Security log you can associate login and logout events to extract a login-duration statistic. The Login/logout events on the Domain Controller are for the individual session that user had with that specific DC, presumably pulling things down like GPOs and other items.
As for software usage, this can also be abstracted out of Windows Eventlogs, but it requires special config and parsing. It requires turning on Process Tracking, and will create VERY large logs on each workstation. You'll then need to extract and analyze those logs to abstract out software usage patterns.
It isn't easy.