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.