I’m a bit of a puritan. I don’t like hundreds of ornate tools. But a few things help.
TextMate is quite good. It’s not free but I consider it worth paying for.
F.lux adjusts the colour temperature of your monitor according to the time of day. I generally have my monitor set quite yellow and low-brightness anyway. Free.
ShiftIt allows you to arrange windows into non-overlapping pre-defined layouts with keyboard shortcuts. Doesn’t beat Awesome window manager http://awesome.naquadah.org/ on Linux, but probably the best possible for Mac OS. Free.
iTerm works a bit better than Terminal.app
Cyberduck does SFTP, S3 and the rest.
Adium is my favourite chat client. Free.
cdto allows you to open a command line prompt from a Finder window. Useful. Free.