i'm hoping that this is the last of my issues in upgrading to 4.5.3.  i appreciate all the responses i've gotten. 

this one seems like something wrong with the core.  the only enabled tasks for the scheduler are dnn ones:

PurgeUsersOnline (every 1 minute / retry 5 minutes)
PurgeScheduleHistory (every 1 day / retry 2 days)
SearchEngineScheduler (every 30 minutes / retry 60 minutes)

i'm seeing scheduler exceptions between every 3 to 15 minutes, and i'm wondering what the duplicate key that is being references in the error message might be? 

7/14/2007 4:47:35 PM   Scheduler Exception       AssemblyVersion: -1; PortalID: -1; PortalName ...

AssemblyVersion: -1
PortalID: -1
PortalName:
UserID: -1
UserName:
ActiveTabID: -1
ActiveTabName:
RawURL:
AbsoluteURL:
AbsoluteURLReferrer:
UserAgent:
DefaultDataProvider:
ExceptionGUID:
InnerException: Add failed. Duplicate key value supplied.
FileName:
FileLineNumber: -1
FileColumnNumber: -1
Method:
StackTrace:
Message: System.ArgumentException: Add failed. Duplicate key value supplied. at Microsoft.VisualBasic.Collection.Add(Object Item, String Key, Object Before, Object After) at DotNetNuke.Services.Scheduling.DNNScheduling.Scheduler.CoreScheduler.AddToScheduleInProgress(ScheduleHistoryItem objScheduleHistoryItem) at DotNetNuke.Services.Scheduling.DNNScheduling.Scheduler.CoreScheduler.WorkStarted(SchedulerClient& objSchedulerClient)
Source:
Server Name: JILLC-WS17

I also suffer from this problem... and from all of my searches it looks like it is due to my having multiple domain names pointing the the same installation of DNN each running from a separate application pool in IIS.

My question is... is it better to accept the errors and have multiple application pools, or possibly suffer some performance reduction by only using one application pool across all domain names?

Yes, having multiple applications pools pointing at the same DNN instance will cause problems with the scheduler firing off multiple tasks doing the same thing.

These same problems happen when trying to run DNN in a web garden (for the same reason).

I don't think it is worth the problems to have multiple application pools hitting one instance.  If you need seperate application pools then you should have multiple instances of DNN also.