One of the huge features we're all looking forward to in Systems Center Configuration Manager 2007 is the ability to drag and drop collections within the MMC. What many of you may not know is that Microsoft has made available a tool named CollTree in the SMS 2003 SDK that allows you to do this in SMS 2003.
You can either download an already compiled version of CollTree from here, or install the SMS 2003 SDK from here and compile the executable from \Program Files\Microsoft Systems Management Server 2003 SDK V3\Samples\VB\CollTree\CollTree.vbp. Be aware that this version only works with SMS 2003; if you're still using SMS 2.0 you would have to use the SMS 2.0 SDK.
Once you have CollTree.exe and you run it, you will need to enter your Central Site Server name and Site Code. If you are using SQL authentication for SMS then you will also need to provide your SQL username and password. Lastly, change the "Drag and Drop Operation" field to "Move Collection" before you hit the Connect button or else you will just be creating a link. Once you click on Connect, CollTree will enumerate your collections and will look something like this:
If CollTree encounters any problems with your collections, then it will prompt you to fix them. You can right-click on the collections to select either "Recover Orphaned Collections" or "Recover Lost Fragments" if necessary. You can choose to delete any links this way also.
To move a collection, simply drag and drop it to the target sub-collection. One caveat: since the CollTree window is not sizable, you may have to collapse some collections with the minus sign to be able to see the collection you want it to move under.
You can also change the drop down to Link Collections and any collections that you drag and drop will then be linked.