I can say this much, this is a very broad question.
There are so many methods and means to do monitor AD because it is multifaceted. As you said, you can use the built-in perfmon tools. Preferably, the better way is to use a monitoring service, such as SCOM (formerly MOM), that will do lots of stuff.
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Some Microsoft tools:
SCOM 2012 - System Center Operations Manager
http://technet.microsoft.com/en-us/library/hh205987.aspx
Monitoring Active Directory Health
http://technet.microsoft.com/en-us/library/cc180912.aspx
Monitoring Active Directory
http://technet.microsoft.com/en-us/library/bb727046.aspx
Microsoft Download details: Ultrasound - Monitoring and Troubleshooting Tool for File Replication Service (FRS):
http://www.microsoft.com/downloads/details.aspx?FamilyID=61acb9b9-c354-4f98-a823-24cc0da73b50&DisplayLang=en
VBscript to return a list of pending replication jobs on a domain controller.
http://activexperts.com/network-monitor/windowsmanagement/scripts/activedirectory/monitoring/
Keeping Track of Changes That Have Occurred Over a Period of Time
http://technet.microsoft.com/en-us/library/cc811562(WS.10).aspx
To check the replication summary you can run repadmin /replsum.
http://blogs.technet.com/b/askds/archive/2009/07/01/getting-over-replmon.aspx
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Scripts:
NUMEROUS scripts are available at the Technet gallery or you can request one based on the customization.
http://gallery.technet.microsoft.com/site/search?f[0].Type=RootCategory&f[0].Value=activedirectory&f[0].Text=Active%20Directory
The Official Scripting Guy Forum is the best resource for script related questions
http://social.technet.microsoft.com/Forums/en/ITCG/threads
If you are looking for assistance with Powershell scripting, you might want to post in the PowerShell forum:
http://social.technet.microsoft.com/Forums/en/winserverpowershell/threads
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Manual methods to look at the health of your DCs:
dcdiag /v > c:\dcdiagDC01.txt (from each DC) (DC diagnostic tool, the /v will test all available tests. Run a /? for specific
test switches)
netdiag /v > c:\netdiagDC01.txt
(Only for 2000/2003 - netdiag isn't supported on Windows 2008 or newer)
repadmin /showrepl [DC01] /verbose /all /intersite (Helps understand the replication topology and replication failures)
repadmin /showrepl dc* /verbose /all /intersite > c:\repl.txt ["dc*" is if you have more than one DC, and the beginning name of the DCs begin with the same name]
repadmin /showrepl dc01.domain.local /verbose /all /intersite> c:\rep-showrepl.txt (Helps understand the replication topology and replication failures)
repadmin /showreps > c:\rep-showreps.txt (This switch shows if partitions have replicated or
not)
repadmin /replsum > c:\rep-replsummary.txt (View replication summary. You can also use the output to create report)
dnslint /ad /s {The DC's IP Address} (From each DC) (http://support.microsoft.com/kb/321045)
nltest /dsgetdc:<domain.local> /force (Tests secure
channels between DCs)
Event log errors from each DC
(Include the Event ID #, "Source Name, and relevant msg in the event)
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There are numerous third party options, too:
ManageEngine OPManager
http://www.manageengine.com/network-monitoring/activedirectory-monitoring.html
Splunk - Monitor AD:
http://docs.splunk.com/Documentation/Splunk/latest/Data/AuditActiveDirectory
Monitor Active Directory
http://www.activexperts.com/activmonitor/functions/adsi/
Using WMI to Monitor AD
http://www.windowsitpro.com/Windows/Articles/ArticleID/41835/pg/2/2.html
Active Directory monitoring and health checkup
http://technetsrilanka.net/blogs/bubble/archive/2009/07/13/active-directory-monitoring-and-health-checkup.aspx
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Last, but not least, previous discussions, some recent, from the DS Forum:
Technet Thread: "scripts, tools to monitor DC" 4/1/2012
http://social.technet.microsoft.com/Forums/en-US/winserverDS/thread/606b62d2-57bc-42af-893f-b2e75f3fb12a
Technet Thread: "Network Monitor and traffic to/from DC" 4/24/2011
http://social.technet.microsoft.com/Forums/en-US/winserverDS/thread/d58e5b52-faab-431b-a01d-b7adf113c1f8
Technet Thread: "AD Performance" 7/11/2009 [Comprehensive responses regarding performance counters]
http://social.technet.microsoft.com/Forums/en-US/winserverDS/thread/48f50a27-82ab-4c1e-aa5a-37fb1e2e6f5b
Technet Thread: "Performance Counter" 11/17/2011
http://social.technet.microsoft.com/Forums/en-US/winserverDS/thread/74a32da6-8ef7-4d01-9330-510c30f72ecc
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