As an outsider, I prefer issue tracking to be in its own application
I recently read Josef "Jeff" Sipek's Email vs. Tool du Jour (via). I broadly agree with Sipek's call to generally use email to other mechanisms, but after mulling over my reaction to one portion of it, I disagree with Sipek over issue tracking, at least some of the time. Sipek says:
First, what about issue tracking? How does that tie into my email-centric world? Well, you can keep your issue tracker, but in my opinion, the comments feature should not be used. [...]
When I work with outside projects or vendors, what I prefer is an issue tracker that holds all the comments in a ticket and also sends a copy to my email. The great advantage of this is that it automatically creates a durable historical record of that issue's discussion (and only that issue's discussion) in one place, one that people (myself included) can refer back to later.
(Sometimes you're referring back to an issue to see what was discussed at the time and hopefully why things were decided as they were. Sometimes you're referring back because an old issue was suddenly revived on you and now you have to remember stuff from two years ago.)
I can create such a durable historical record myself with email, but to do that I would have to create a folder or a tag or whatever for each issue and then carefully file all email in the right way. I would rather have an issue tracker do this for me, and in the process provide a convenient identifier for the whole issue (a URL, a bug number, etc). The natural state of email is a big pile, which goes badly with wanting to keep track of a bunch of things separately so you can find them (and just them) later.
With that said, we don't use an issue tracker here, although we do archive all of our group discussion email for later reference. I think one difference is the volume involved (we send a lot more email and have a lot more discussions than I do when I interact with outside projects) and another is that we feel many of the issues we deal with are ephemeral and will never need to be looked back at (and won't be revived suddenly in three months, although it sometimes happens).
(And if we did have an issue tracker, I would very much want to interact with it by email since we basically live in email as it is.)