normal timer / stopwatch / alarm

• Alarm Clock by Tarry91 — almost as flexible as TimeLeft, but FREE
• TimeLeft (yes, it has a $25 version, but the freeware version doesn't have any nag screens (see last two questions here). And it really is pretty damn flexible.)
  • if you want a better alarm audio file, use listentoyoutube.com/vidtomp3.com/2convert.net on one of the klaxon youtube videos
• Marxio
• Multi-Timer
• Cool Timer
• Work Break Timer
• MORE
• more

project time tracker

• Tiny Time Tracker — I've used it a lot, it's great, as long as you want a light-weight no-frills tracker
• SlimTimer.com

encourage productivity

• ProcrastiTracker
• Skrommel's TakeABreak (needed to be modified a fair bit, buth to fix odd behavior, and to taylor to my needs)
• Temptation Blocker
• browser
  • TimeTracker