LinkABoo

LinkABoo is an application that is able to create hyperlinks which point to specific e-mail messages inside Apple's "Mail" application.

If you are tired of searching e-mails by sender, date, and subject (which is still tedious, even in times of "Spotlight"), then LinkABoo is for you. Using LinkABoo, you can refer to an e-mail with the ease of a single mouseclick.
Links created by LinkABoo can be used just like any "regular" hyperlinks (because that's what they are) on Mac OS X. For instance, you could create a linked Internet location file (URL clipping file) in the Finder, put it on the Dock, add the link to an iCal todo, use it from applications such as OmniOutliner, DEVONthink or Yojimbo, or even link to an-email it from the shell. Basically, you can create and utilize such links in any Mac OS X application or context where you can make use of hyperlinks.
And, of course, LinkABoo does neither modify "Mail" nor your e-mails, and it does not install any background process: it only runs when you use it to create a link, or when you click a LinkABoo link. LinkABoo does not alter the way Mail works, and thus it will have no effect on Mail's stability.