Second domain controller crashed today and will not boot back up. How can I clean up active directory 2008r2??

You need to seize the FSMO roles from the dead server.
Seize FSMO roles
To seize the FSMO roles by using the Ntdsutil utility, follow these steps:

    Log on to a Windows 2000 Server-based or Windows Server 2003-based member computer or domain controller that is located in the forest where FSMO roles are being seized. We recommend that you log on to the domain controller that you are assigning FSMO roles to. The logged-on user should be a member of the Enterprise Administrators group to transfer schema or domain naming master roles, or a member of the Domain Administrators group of the domain where the PDC emulator, RID master and the Infrastructure master roles are being transferred.
    Click Start, click Run, type ntdsutil in the Open box, and then click OK.
    Type roles, and then press ENTER.
    Type connections, and then press ENTER.
    Type connect to server servername, and then press ENTER, where servername is the name of the domain controller that you want to assign the FSMO role to.
    At the server connections prompt, type q, and then press ENTER.
    Type seize role, where role is the role that you want to seize. For a list of roles that you can seize, type ? at the fsmo maintenance prompt, and then press ENTER, or see the list of roles at the start of this article. For example, to seize the RID master role, type seize rid master. The one exception is for the PDC emulator role, whose syntax is seize pdc, not seize pdc emulator.
    At the fsmo maintenance prompt, type q, and then press ENTER to gain access to the ntdsutil prompt. Type q, and then press ENTER to quit the Ntdsutil utility.

For more details see:
http://support.microsoft.com/kb/255504

Once complete you can remove the  dead DC
To remove dead or orphaned D.C. you can go to Active Directory Users and Computers, then go to Domain Controllers OU, then you will see the list of Domain Controllers you can directly delete it with the following options which tells you what is the right action you will do, and don't forget to go to Active Directory Sites and Services to fully delete also the DC which is no longer use and no longer active to eliminate the error messages like NTDS.

     If you have also a Windows Based DNS Server delete also these entries at Forward Lookup Zones:

     1.)  (same as parent folders)   (Host A)   <IP Address of the dead Domain Controller>
     2.)  <DC Server Name>   (Host A)   <IP Address of the dead Domain Controller>

     At Reverse Lookup Zones:

     1.)  <IP Address of the dead Domain Controller>   Pointer (PTR)   <mydomain.com>

Please refer to following links:

http://support.microsoft.com/kb/324801
http://support.microsoft.com/kb/255504
http://social.technet.microsoft.com/wiki/contents/articles/6736.move-transfering-or-seizing-fsmo-roles-with-ad-powershell-command-to-another-domain-controller.aspx

The second part of Craig's answer is known as a "metadata cleanup"  more iformation on that here

http://technet.microsoft.com/en-us/library/cc816907(v=ws.10).aspx#bkmk_graphical

How many DCs do you currently have up and running?

Thanks

Mike

I only have one more DC on this subnet, but 4 more DCs are located in 2 other offices and one newly introduced "sickly" DC in another new office. The last DC is another story and I have another thread going to try and clean that up, although my "sickly" DC probably has to be demoted and reinstated, I have no replication working on it. But to answer your question, I now have 5 functioning DCs on my network and only one in my home office

ok good so you have more than 2 so that is why I asked.  

Thanks

Mike