I also use Captur (http://cambhlumbulunk.blogspot.com/p/captur.html) for taking screenshots since I can never remember the obscure OS X shortcuts.
If you need more, grab Pixelmator. It's an excellent program for basic image manipulation and drawing. If you need professional level tools, grab Paint Tool SAI, Photoshop, or GIMP as you need. Pixelmator will not be a good replacement for this programs.
* Click the pen in a box button next to the search bar. A new toolbar will appear.
* Click the rectangle button between the wand and the oval. Three new buttons will appear. If you mouse over them you can see what they do.
* Draw a rectangle around the area you want to highlight.
* Click the fill color button (it's right next to the border line thickness button)
* Choose "Show Colors..." from the color menu that pops down.
* Select any color and any opacity of that color to fill the rectangle
Here's a of keyboard shortcuts for taking screenshots: http://support.apple.com/kb/ph11229 These shortcuts will put the images on the desktop.
I prefer to use a little tool call SnapNDrag to do screenshots. It's $10 on the app store: https://itunes.apple.com/us/app/snapndrag-pro/id430397512?mt... It's a simple app on top of the operating system's existing functionality. It's just a fancier version of the built in Grab.app.
(Also, if you haven't looked into Alfred or Quicksilver for app launching, I recommend it.)
https://www.evernote.com/shard/s16/sh/0d23774d-cbb7-433d-8af...
1. https://itunes.apple.com/us/app/skitch-snap.-mark-up.-share....
Edited to add: BTW, Shift+Cmd+4 is a super useful shortcut from taking screen grabs on the Mac.
Of course, it's not cheap, but I suspect you're more interested in the best rather than the cheapest tool.