Don't think so. I don't use Mail.app, but you are probably overthinking this a bit. Pretty sure Spotlight will index email messages in Mail.app and so you could search for it that way.
Otherwise, I know that Mozilla Thunderbird 3.0 has a sort of "Googlefied" system where you can search for messages quite quickly. Thunderbird also has a method for "starring" messages to let you find them even faster. Might want to consider making the switch if Spotlight doesn't index Mail.app's mailboxes.
Alternately, you could make a new email folder, and place copies of important messages in there. It doesn't really solve the underlying problem, because too many important messages and you're right back where you started. But so long as you keep the number of important messages to a minimum, it could work.
Is there anyway to highlight an already read and saved message in Mac Mail?
To clarify, when I open Mail I have a window that shows all my incoming messages, both unread and read. Sometimes after I read a message I want to be able to go back and quickly find it. This could be several days later and in the meantime I have 50 more saved messages and trying to find it is difficult.
Is there some way to highlight it in color or flag it so I can easily go back and find it?
I am running 10.5.8 although I doubt that has any bearing on anything.