When writing code in C++ or Java using emacs I notice that I can get the code all nicely aligned and indented correctly by simply adding a comment at the end of each line of code. As you enter the //, the line of code moves to its correct alignment. What I have been doing is writing my code and periodically tidying it up by adding // at the end of every line of code. My question is, can I speed this aligning and indenting process up by formatting the entire file using one command? Emacs obviously knows how much each line should be indented, but doing it one line at a time by adding // is laborious.

You can press TAB and the line you are currently on should get indented. You can also select a region with C-space to mark the start of the block , moving the cursor to the end of the block and then doing "M-x indent-region".

Even faster, use C-x h to highlight everything, then C-M-\ to re-indent it. Also, C-j normally does a newline-and-indent type function (for most modes; not Emacs Lisp Interaction though). If you want to do a sort of auto-indentation for certain modes, you can bind the RETURN key to do indentation like so:
Just list whatever modes you want to apply it for in that last list with all the mode names in it. This is what I use for almost everything. When you hit RETURN, it reindents the current line, moves you down to the next line, and auto-indents there. Very useful.