Atlassian is really the Major Grower in this space - good sized developer community, and "App Store" equivalent (Plugin Exchange ) - They have about 50,000 plugins a month downloaded from a library of 400 - 130 of which are for Jira.
The latest rev of their product, Jira 4.0, has one major feature - a SQL like query engine, they call it "JQL" - Jira Query Language - which allows you to do everything you might expect/imagine. Their searching was _already_ better than FogBugz, but JQL makes you not even not want to compare the two.
Interesting Notes:
Google for "Bug Tracking Software" doesn't bring up FogCreek, but does bring up Atlassian.
Atlassian is like the "Anti-Fog Creek" in terms of it's thoughts around office. I've been to their San Francisco Offices (which are supposedly like their Sydney) - One Big Wide Open Space. No Cubicles. No Offices. Nothing - just pure Agile openness.
Go to Atlassian.com - you are 4 Clicks away from having the software on your computer, and it takes about as many seconds. And it figures out whether you want OS X stuff, linux files, etc...
Go to FogCreek.com - 30 seconds later I _still_ couldn't figure out where to click to try their stuff - and when I do, I finally land on a page where I need to start providing Email Addresses, Phone Numbers, accepting terms of services. It's almost like they are _daring_ you to try the competition.
What's cool, is that _both_ Fog Creek and Atlassian are the ultimate results of Startups going head-head. Someone will have to write a book about these two companies.
http://www.atlassian.com/about/history.jsp Atlassian: "In 2002, fresh out of university, Scott Farquhar and Mike Cannon-Brookes, With total start up costs of $10,000 charged to a Visa card, they built JIRA, a professional bug and issue tracker, and Atlassian was born. By 2004 the company had grown to six developers."
http://fogcreek.com/About.html Michael Pryor founded Fog Creek Software with Joel in September 2000.
Fog Creek's Major Problem, and the reason why I suspect Atlassian is going to wipe them out if they don't get their Act Together, is that Fog Creek has, to my knowledge, three products:
o Bug/Project Management/Software Project Tracker (fogbuz)
o VNC Hosting Service for Tech Support (Copilot)
o Forums for Software Developers/SysAdmins StackOverflow/ServerFault
o 25 Employees
o Issue Tracking Software (jira)
o Wiki (confluence)
o Source Code Reviewer (fisheye)
o Code Review (crucible)
o Continuous Integration (bamboo)
o Code Coverage (clover)
o Identity Management (Crowd)
o 200 Employees
o 15,000 Customers
http://www.atlassian.com/about/customers.jsp