Cheaper / free alternative to MailTags

You could try the 'flag' option in Mail. To see only flagged mails, you could create a smart folder that shows only flagged mails. Alternatively, from view menu, check the option to show the flags column and you can then click on the column to sort flagged mails.

Open the relevant mailbox. Select a message or messages (without opening).

From the 'Format' menu choose 'Show Colors'. You will get the usual colour selector; select a colour and it will be applied to the message(s) in the list. As many colours as you like.

When you have selected a colour you want to use again drag it from the display field at the top of the pane to the grid below the colour wheel to save it as a favourite, so you don't have to try to match it manually in future. (If the grid doesn't show drag the dot at bottom centre of the pane downwards.)

You are right that you hv only one flag option, which is flag or not, kind of binary. You might be able to color the messages if not the flags.

While the post above by wilmut is one way.

To automate it, you might want to create a rule which will color msg with certain characteristics like sender address, or subject word and so on.

You can then combine a smart mailbox to collect all flagged and then you might pick msgs by color.