I have found that large tools that integrate a lot of functionality over different domains almost always have a short lifespan before something new and awesome comes up providing a better alternative for large subset of that functionality. But small focussed tools tend to live around in my toolbelt a lot longer.
So here is my list, this is almost certainly biased towards web-development - as that is primarily where my interest lies and what my job involves:
Emacs: Editor for all things that need editing. Runs everywhere. Can be used to run everything. Has an extension for almost everything. Keyboard driven interface. Effortlessly handles hundreds of buffers.
Sip: (OS X specific - itunes link) Versatile color picker with a minimal interface. Copies color in exactly the format you need.


Git + SourceTree: Git is amazingly useful on its own. But sourcetree is invaluable for visually exploring the history - good integrated search, runs on windows and mac.
licecap: Records sections of screen as Gifs - invaluable for discussing UX decisions over emails or issue tracker threads. Has dramatically reduced the time I used to spend on boring UX meetings where people would keep bike shedding over mundane aspects over hours.
All the above programs are free.