Almost everyone I talk to seems to be using WebEOC as their incident management tool. There are other solutions out there, but I don't hear much about them. Not everyone is happy with WebEOC.
If you are one of the unhappy :( people or organizations, you might want to check out COBRA by Dynamis, with this link providing a PowerPoint overview of the system. What caught my attention is that the nation of Belgium has adopted this system, from stem to stern.
We have not been able to achieve the same level of adoption — by any system here in Washington state. Most jurisdictions are using WebEOC, but there is little to no integration between emergency operations centers (EOC) for larger counties or between local jurisdictions and the State EOC.
Every once in a while, a new system pops up that is home-grown and is successful in one geographic region, but going beyond the "local-regional" area is tough to accomplish.
Check out COBRA and see if it fits the bill for you and your organization.