I don't really know if there is a good way to get up to speed with the OS, other than just using it. Familiarity will come with experience; At least I've always found that the best way to get familiarized with a new OS (or any software) is to acknowledge that I will probably not be as effective during the inevitable period of adjustment, and try to perform tasks that I knew how to perform with the preceding tool.

Here is a short list of various software on my mac I find very useful:

- AppCleaner (http://www.freemacsoft.net/appcleaner/): Removes files and preferences associated with applications you wish to uninstall.

- Amethyst (https://github.com/ianyh/Amethyst): The only fully functional dynamic tiling window manager I've found that works well under OS X.

- f.lux (https://justgetflux.com): Change display color temperature according to time of day.

- Moom (http://manytricks.com/moom/) [or Divvy/SizeUp/...]: Manage, move and resize window with keyboard.

- Menumate (http://zipzapmac.com/menumate): Trigger menu bar with hotkey.

- Shortcat (https://shortcatapp.com): Goto anything on the screen via keyboard, sort of a fuzzy finder for the UI,

- iTerm2 (http://iterm2.com): Alternative terminal emulator.

- MAMP (http://www.mamp.info/en/ Apache, MySQL and PHP stack.

- Coda (https://panic.com/coda/): Very nice editor, particularly for frontend webdev, as it includes page preview functionality, as well as some other tools. Alternatively, your editor of choice.

- Cakebrew (https://www.cakebrew.com): GUI for homebrew.

You should also check out brew cask (http://caskroom.io), which enables you to install binaries via homebrew.

P.S. As your question is very broad indeed, I think you might get more responses if you asked a few narrower questions or described some specific problem.