A great (completely freeware) program is ToDoList Resources. It does time tracking through an on/off button for each task (the tiny clockface by the "Time Spent" field is the on/off button. Here's a screenshot of the main program, followed by a screenshot of the time options dialogue box:
I've always found lots of benefits to time management and time tracking in particular, but not found a tool that was both simple, intuitive and powerful enough for all my needs. Lots of people don't enjoy time tracking, and I think the tools are partly to blame.
I've tried online and downloadable versions of lots of similar programs off and on for years, and the AllNetic Working Time Tracker is my favorite. I even coded up a custom program when I couldn't find anything I liked (but this is better).
My review? I love how easy and intuitive this thing is. For example, it pops up "Looks like you stopped working a while ago; how would you like to account for recent time" and then gives you useful one-click choices. Of course, it also runs automatically, allows creating reports and invoices, and much more.
It pops up either manually or automatically from the Windows notification area (what Microsoft used to call the system tray), those tiny icons in the bottom right of your screen on Windows systems. And you can run it in it's own Window for working with reports or setting up projects with subtasks.
Time tracking is done separately for each task on a project. You choose a task you are working on and switch on the time tracking.
Just try it! You won't need the manual. Download the shareware version and give it a go. Here are a few screenshots: