If you're looking for a comprehensive time tracking alternative, CreativeWorx TimeTracker has a desktop application in addition to a browser version. There's a new desktop application being released in about a week, and it's killer! Check it out: www.creativeworx.com
If you want automatic time tracking with durations, see if CreativeWorx TimeTracker fills the bill. It automatically activities within applications (Office, Adobe Creative Suite, Apple productivity, browsers) plus your calendar events. www.creativeworx.com
CreativeWorx TimeTracker is an automatic time capture tool that can handle most of what you need right away. The cool part is not that it captures what your employees do (for their eyes only) but that it learns their job codes and saves them so much time.
As for the punch in/out: A user could easily mark time in/out by clicking on the timesheet. If TimeTracker users need a simple app or UI to enter the time in/out, that could be easily added by us or via our API.