I just wrote an article in French regarding recommanded application pool configuration for the SMP and IIS.

It's available [1] but I won't tease you too much. Here is the most interesting part from it, a batch script to automate the pool creation, "straight off the bat" as a British friend of mine would put it. Please note that some web-applications work nicely in their own pools, but other need to remain in the /Altiris application domain. So if you feel like trying to craft your own, keep this in mind and be ready to revert.

@echo off
set appcmd=%comspec%\..\inetsrv\appcmd

%appcmd% add apppool -name:Altiris-NS-Agent
%appcmd% set apppool Altiris-NS-Agent -managedPipelineMode:Classic
%appcmd% set app "Default Web Site/Altiris/NS/Agent" -applicationPool:Altiris-NS-Agent

%appcmd% add apppool -name:TaskManagement
%appcmd% set apppool TaskManagement -managedPipelineMode:Classic
%appcmd% set app "Default Web Site/Altiris/TaskManagement" -applicationPool:TaskManagement
%appcmd% set app "Default Web Site/Altiris/ClientTaskServer" -applicationPool:TaskManagement

%appcmd% add apppool -name:ActivityCenter
%appcmd% set apppool ActivityCenter -managedPipelineMode:Classic
%appcmd% set app "Default Web Site/Altiris/ActivityCenter" -applicationPool:ActivityCenter

%appcmd% add apppool -name:PatchManagement
%appcmd% set apppool PatchManagement -managedPipelineMode:Classic
%appcmd% set app "Default Web Site/Altiris/PatchManagement" -applicationPool:PatchManagement
%appcmd% set app "Default Web Site/Altiris/PatchManagementCore" -applicationPool:PatchManagement
%appcmd% set app "Default Web Site/Altiris/PatchManagementMac" -applicationPool:PatchManagement

%appcmd% add apppool -name:SoftwarePortal
%appcmd% set apppool SoftwarePortal -managedPipelineMode:Classic
%appcmd% set app "Default Web Site/Altiris/SoftwarePortal" -applicationPool:SoftwarePortal

%appcmd% add apppool -name:ITAnalytics
%appcmd% set apppool ITAnalytics -managedPipelineMode:Classic
%appcmd% set app "Default Web Site/Altiris/ITAnalytics" -applicationPool:ITAnalytics
%appcmd% set app "Default Web Site/Altiris/ITAnalyticsCSMP" -applicationPool:ITAnalytics
%appcmd% set app "Default Web Site/Altiris/ITAnalyticsSEP" -applicationPool:ITAnalytics

[1] https://www-secure.symantec.com/connect/fr/articles/gestion-des-pools-applicatifs-iis-pour-smp-71