Web Design & Excel Spreadsheet Design
First of all, I'm very honest. If I'm working on an hourly basis, to keep track of my time, I log in and out with an Excel workbook I made. This allows me to keep track very accurately and also helps to determine future quotes. I typically work from home, so this time-keeping method also means that you don't pay for me to let the dog out!
If I work on an hourly basis, when I start work on a site, I will ask for people to give me a stop point. This enables them to have control of the project by telling me, for example, "Put in 10 hours and let me review." When I am nearing this amount of time, I will let them know and they can decide what the next step will be.
Firm quotes have no time limits, but any additional work not in the quote will have to be quoted separately.