I switched to ripgrep for my grepping needs, I find it fast and the syntax and output coloring handy.
Just found fastmod recently, https://github.com/facebookincubator/fastmod. Very handy for doing bulk substitutions of strings in project directories - it can prompt with a diff for every change and do full regexes, so you can try out tricky things and make sure it isn't doing anything crazy before you let it make 500 changes throughout your repo.
Also a fan of gitsh, https://github.com/thoughtbot/gitsh. Helps out with using Git on the command line just the right amount IMO - just avoiding the git prefix, tab completion, and a little syntax highlighting, instead of trying to redo the whole interface.
I don't use it that much, but jq, https://stedolan.github.io/jq/ is really handy for slicing and dicing json data without diving into the complexity of writing actual programs.
And on OS X, homebrew is indispensable for actually managing all of your CLI programs.
I also have found this Google Drive cli handy, https://github.com/odeke-em/drive. If you want to sync some but not all of your Google Drive files, and only push and pull on command instead of continuously, it's great.