To manually install or reinstall the .Net framework in IIS,   Run ASPNET_REGIIS.EXE -I –Enable

Note that on an X64 machine you can install this from either a 32 or 64-bit directory.  A typical path is something like;
C:\WINDOWS\Microsoft.NET\Framework\v2.0.50727

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Set and view IIS6 Isolation Mode:

2 Modes:

• Worker Isoation Mode, which is default, and
• IIS isolation mode for older apps that are incompatible with Worker IsolationMode  (needed for WOW64)

To get current mode from command prompt:

CSCRIPT %SYSTEMDRIVE%\Inetpub\AdminScripts\adsutil.vbs get W3SVC/IIs5IsolationModeEnabled

To configure the server to run in worker process isolation mode:

cscript %SystemDrive%\Inetpub\AdminScripts\adsutil.vbs set W3SVC/IIs5IsolationModeEnabled FALSE •

To configure the server to run in IIS 5.0 isolation mode:

cscript %SystemDrive%\Inetpub\AdminScripts\adsutil.vbs set W3SVC/IIs5IsolationModeEnabled TRUE

Knowledgebase article for more info

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