Several of the other answers say that it doesn't matter what the system is written in, and i can't agree with that.
They are probably right when it comes to simple desktop applications (for example, we use Mercurial/TortoiseHG for source control and it really doesn't matter that it's written in Python...it just works).
But it's completely different when the application needs some kind of special server (web server, database server...most available bug trackers need both).
When you need some of those, you will probably use something you know:
For example, we are a Microsoft shop...we already have ASP.NET web servers and SQL servers ready and running and we have people who know how to use them.
On the other hand, there's no one here who knows anything about, say, Oracle/MySql/PostgreSql or Ruby/PHP.
This rules out quite a lot of the available bug trackers because we have no idea to even get them to run!
Yes, we could try & error and setup new web and database servers and try to get the stuff working, but it's hard to justify learning all the stuff just to run a simple bug tracker.
(and just installing and getting it to run is not all you need...for example, when you have the database running, someone has to figure out how to take backups, how to restore them in case something goes wrong...the list goes on and on)
So we will probably use a .net bug tracker (we are just evaluating ourselves)...probably Bugtracker.Net.
EDIT:
John, that's not what I meant.
For example, besides Bugtracker.Net I evaluated Redmine as well (which is written in Ruby on Rails).
I don't want to change anything in the Redmine code, just install it - but take a look at the installation instructions:
Even to get Redmine installed, you need a certain level of knowledge about RoR (which I don't have at all, neither any of my co-workers - we are Windows and .net users and no one of us has ever used Ruby).
Maybe Redmine is cooler than BugTracker.Net or can do more - but can we really justify learning some RoR just to be able to install this one piece of software?