1. Microsoft Exchange Best Practices Analyzer (ExBPA)
ExBPA was released in September 2004 and there are still numerous companies who have not yet incorporated running the tool into their routine maintenance procedures. It is strongly recommended that ExBPA be run regularly against your entire Exchange environment.
ExBPA gathers a huge amount of data about your environment from various locations including Active Directory, the registry & metabase on your Exchange Servers, and WMI. The tool compares the configuration of your environment against Microsoft best practises and reports on where your configuration has been altered from the default and where this clashes with best practise.
ExBPA is available for download from http://www.exbpa.com
Winroute is a less common tool but I think should also be used on a regular basis, although not perhaps as often as ExBPA. It is useful in understanding the routing topology of your environment and anything that may have changed. Winroute connects to the Exchange Server you specify (for routine use of the tool run it against each Routing Group Master) and presents the link state information that is held in memory on that Exchange Server.
3. Performance Monitor
One of the 'Administrative Tools' included with Windows Server. In my experience performance monitor is one of those tools with which you can collect so much useful information that what you end up with is confusing and counter productive. To assess the performance of an Exchange Server is actually very easy - you only need to collect a small subset of counters and once you are sure you are happy with the performance of your server, the assessment of routine performance baselines should not take you any time at all.
You might also consider using ExTRA. The 'Exchange Performance Troubleshooter' is included within ExTRA and is a good place to start if you suspect you have a specific performance issue. I don't think this should replace using Performance Monitor though.
4. Microsoft Baseline Security Analyzer
MBSA is a great tool which can be used to detect common security misconfigurations and missing security updates on your Exchange Servers. MBSA is compatible with Microsoft Update and Windows Server Update Services and the SMS Inventory Tool for Microsoft Update. It should not be relied upon as the sole tool in your environment for determining patch status for example as it relies on manual intervention to run each time. However as a one off for a health check, or if used as a routine way to assess the security of your Exchange Servers it is a fantastic tool. Install the tool on your workstation and run it against each of your Exchange Servers in turn.
More information about MBSA and a location for downloading the tool can be found here: http://www.microsoft.com/technet/security/tools/mbsahome.mspx
5. Microsoft Operations Framework Self-Assessment Tool 2.0
I will include the MOF Self-Assessment Tool here as it is useful if you are looking at the operational procedures surrounding your Exchange environment. However this is only a start and much more is required if you are looking at Exchange Server specifically. The tool is available from here; http://www.microsoft.com/technet/solutionaccelerators/cits/mo/mof/moftool.mspx
..'Run your own Exchange Server Health Check.... Part 1 - Operations' to follow soon...