* TotalFinder (makes the OS X finder not terrible anymore, tabs, etc)
* HandsOff/LittleSnitch (oh, you're just using the built-in firewall? that's cute.)
* Transmit (everything you could ever want in an FTP app)
* CommandQ (W and Q are way too close together)
* Mou (free alternative to Byword)
* Evernote (note-taking that syncs absolutely everywhere)
* Alfred (modern day Quicksilver)
* Growl (notify me of all the things!)
* AppCleaner (good for finding the random left-behind files)
* ClipMenu (clipboard history and saved text snippets all in one)
* f.lux (less eyestrain for marathon coding sessions)
* GasMask (easy hosts file changing)
* GrabBox (automatically saves screenshots to my DropBox public folder and copies the URL to my clipboard? YES PLEASE. replaces the need for CloudApp, etc.)
* Sublime Text 2 (cross-platform and modern TextMate/BBEdit/Vim all rolled into one amazing editor)
* SourceTree (good and free Git/hg front-end)
* Witch (finally a better Cmd-Tab)
* Moom (window tiling and profiles galore)
* Hyperdock (dock previews and drag-to-edge window resizing)
* Prey (stolen goods tracking)
* Textual (IRC)
* Adium (chats)
In terms of my actual command-line environment:
* iTerm2
* Homebrew
* (way too many individual commands to list here)
Also Chrome/FF extensions can get you some really great paid native app replacements, like RestConsole (no more need for Http Clients).