The following are the registry edits I have done to my computer to all but eliminate the use of Windows Explorer. It is quite annoying to have to click a special icon to get TC instead of just being able to open any folder or drive or even My Computer or My Documents etc. and this registry file should solve the problem. Of course, edit it to work with your configuration (like where you put TC and what command line options you want)
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Windows Registry Editor Version 5.00
[HKEY_CLASSES_ROOT\Directory\shell]
@="open"
[HKEY_CLASSES_ROOT\Directory\shell\open]
[HKEY_CLASSES_ROOT\Directory\shell\open\command]
@="\"C:\\totalcmd\\TOTALCMD.EXE\" \"%1\""
[HKEY_CLASSES_ROOT\Drive\shell]
@="open"
[HKEY_CLASSES_ROOT\Drive\shell\open]
[HKEY_CLASSES_ROOT\Drive\shell\open\command]
@="\"C:\\totalcmd\\TOTALCMD.EXE\" \"%1\""
[HKEY_CLASSES_ROOT\Drives]
[HKEY_CLASSES_ROOT\Drives\shell]
[HKEY_CLASSES_ROOT\Drives\shell\open]
[HKEY_CLASSES_ROOT\Drives\shell\open\command]
@="\"C:\\totalcmd\\TOTALCMD.EXE\" \"%1\""
[HKEY_CLASSES_ROOT\CLSID\{20D04FE0-3AEA-1069-A2D8-08002B30309D}\shell]
@="open"
[HKEY_CLASSES_ROOT\CLSID\{20D04FE0-3AEA-1069-A2D8-08002B30309D}\shell\open]
[HKEY_CLASSES_ROOT\CLSID\{20D04FE0-3AEA-1069-A2D8-08002B30309D}\shell\open\command]
@="\"C:\\TOTALCMD\\totalcmd.exe\" \"C:\\Documents and Settings\\mds00\\Desktop\""
[HKEY_CLASSES_ROOT\CLSID\{450D8FBA-AD25-11D0-98A8-0800361B1103}\shell]
@="open"
[HKEY_CLASSES_ROOT\CLSID\{450D8FBA-AD25-11D0-98A8-0800361B1103}\shell\open]
[HKEY_CLASSES_ROOT\CLSID\{450D8FBA-AD25-11D0-98A8-0800361B1103}\shell\open\command]
@="\"C:\\TOTALCMD\\totalcmd.exe\" \"%1\""
[HKEY_CLASSES_ROOT\CLSID\{208D2C60-3AEA-1069-A2D7-08002B30309D}\shell]
@="open"
[HKEY_CLASSES_ROOT\CLSID\{208D2C60-3AEA-1069-A2D7-08002B30309D}\shell\open]
[HKEY_CLASSES_ROOT\CLSID\{208D2C60-3AEA-1069-A2D7-08002B30309D}\shell\open\command]
@="\"C:\\TOTALCMD\\totalcmd.exe\" \"::{208D2C60-3AEA-1069-A2D7-08002B30309D}\""
Basically all I did was created a new shell command called open on each of these items and made it the default action. So, I think you could actually call it whatever you want, such as open with TC and it would still work. Some of the entries like Directories work fine using the %1 option to open the directory in TC, but some of the special folders don't seem to like that like My Network Places, which is why I used that ugly long key name. My Computer is not really a folder either and wouldn't open in TC so I just set it to my Desktop Folder, so really you could set any of your special folders to open any folder you want. I tried to use %userprofile% to go to the current user's desktop but it didn't seem to work, so I just set it to my actual path since I'm the only person using this computer anyway

If anyones got any ideas on how to fix the %userprofile% thing I'd like to use it instead.
*** EDIT ***
Well, I looked into it a little more and it seems you can get My Computer to work under TC... Instead of using the above section listed here
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[HKEY_CLASSES_ROOT\CLSID\{20D04FE0-3AEA-1069-A2D8-08002B30309D}\shell\open\command]
@="\"C:\\TOTALCMD\\totalcmd.exe\" \"C:\\Documents and Settings\\mds00\\Desktop\""
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[HKEY_CLASSES_ROOT\CLSID\{20D04FE0-3AEA-1069-A2D8-08002B30309D}\shell\open\command]
@="\"C:\\TOTALCMD\\totalcmd.exe\" \"::{20D04FE0-3AEA-1069-A2D8-08002B30309D}\""