There are two tags:
Neither have tag wikis and frankly I don't know which of them to use. Is there a difference?
terminal is for the actual GUI program,
pantheon-terminal. Use this tag when configuring it, like changing the transparency, text colour or font etc.
Command line is for running commands - this could be using any terminal -
pantheon-terminal. Whichever it is, if this tag is used, the terminal being used shouldn't matter. Anything tagged command-line should apply to any bash terminal.
Yes, there is a difference between “command line” and “terminal”. The most relevant difference, in fact, is between shell and terminal. The shell is the program that interprets commands. It's also the program that displays a prompt and provides facilities to edit commands when you type it. Bash is the default shell; there are others. The terminal (more precisely a terminal emulator) is the program that provides basic character input/output. Pantheon Terminal is the default terminal emulator programs; there are others.
What does this mean in terms of tags? Given that the command line is not the primary focus of this site, I think it would make sense to have a tag command-line that covers all command line issues, whether they're with bash or with the terminal (most issues are with the shell anyway).
There shouldn't be a tag shell, but there should be a tag bash for bash-specific issues such as prompt settings, command history, command line editing, etc. There should also be a tag shell-script for when the shell is used to run scripts rather than interactively.
This isn't the tags we use on Unix & Linux — there we strictly distinguish between generic shell use ([shell]), features of specific shells ([bash], etc.), terminal issues ([terminal]), features of specific terminal emulators ([xterm], etc.), and we have a tag [command-line] that we don't quite know what to do with. But U&L has a very different audience — primarily command-line-based — so different tags are warranted.