Applications launching extremely slowly - Mac Pro, OSX 10.6.8

Hi,
I have tried everything I can think of but perhaps some of the experienced people on this forum have seen this before. I have a Mac Pro about a year old and everything was running fine until about 2 weeks ago. The applications take extremely long to start up and settle down but eventually they do. Entourage, for example, takes 10 minutes or longer. The computer boots normally though.
Once everything has settled down they seem to run just fine but starting any new application will take a very long time. The curious thing is that after boot the first couple of applications seems to load up a usual but after that things slow down. I can't detect anything unusual in the activity monitor and the affected apps show up as "not responding" but if you wait long enough that notification goes away and they seem to work fine.
I have firewire connected to a Protools Digi 002 rack and Ethernet connected to a Time Capsule, USB connections are a 24" Cinema display and mouse.
The machine is an 8 Core 2.4 Ghz, 6 GB RAM (4.36 GB free ), 1TB HD (700 GB Free)
This is what I have done to attempt a fix:
Restore from a Time Machine backup from several days prior to the start of the incident (1 week ago). 
Re-install OSX 10.6.8 combo update 
Delete and restore various applications (like MS Office 2008). 
PRAM/SMC reset 
Techtool Pro complete test suite scan including disk surface scan, directory rebuild and optimization 
Flush the Cache 
Rebuild Permissions (several times)
So far nothing has solved the issue. My next step was to try here and then do a complete re-install from the ground up (erase HD, install OSX, install applications). I didn't want to take that step unless there was no other alternative because it is a pain.
Also it does not answer the question of "what is wrong" so I can avoid it again so if anyone has any clues/suggestions/sage advice I would greatly appreciate it.
Cheers,
JdanS

Hi Linc,
Thanks for the suggestion. I forgot to add that to my bullet point list (I tried it already) but to be thorough I followed the steps again.
The results are the same but while I was waiting for Entourage to load (23 minutes this time btw) I ran a sample on the process under the activity monitor.
Not sure if this adds any value but here is the output:
Sampling process 164 for 3 seconds with 1 millisecond of run time between samples
Sampling completed, processing symbols...
Analysis of sampling Microsoft Entourage (pid 164) every 1 millisecond
Call graph:
    2759 Thread_1492   DispatchQueue_1: com.apple.main-thread  (serial)
      2759 start
        2759 _start
          2759 main
            2759 LApplication::Run()
              2759 LApplication::ProcessEvents()
                2759 RunApplicationEventLoop
                  2759 ToolboxEventDispatcher
                    2759 SendEventToEventTarget
                      2759 SendEventToEventTargetInternal(OpaqueEventRef*, OpaqueEventTargetRef*, HandlerCallRec*)
                        2759 DispatchEventToHandlers(EventTargetRec*, OpaqueEventRef*, HandlerCallRec*)
                          2759 ToolboxEventDispatcherHandler(OpaqueEventHandlerCallRef*, OpaqueEventRef*, void*)
                            2759 SendEventToEventTargetWithOptions
                              2759 SendEventToEventTargetInternal(OpaqueEventRef*, OpaqueEventTargetRef*, HandlerCallRec*)
                                2759 DispatchEventToHandlers(EventTargetRec*, OpaqueEventRef*, HandlerCallRec*)
                                  2759 EventLoopEventHandler(OpaqueEventHandlerCallRef*, OpaqueEventRef*, void*)
                                    2759 LApplication::PostProcessEventsRAEL(OpaqueEventRef*, OpaqueEventTargetRef*, unsigned char)
                                      2759 LPeriodical::DevoteTimeToIdlers(EventRecord const&)
                                        2759 RegisterWithSAUIdler::SpendTime(EventRecord const&)
                                          2759 McpRegisterWithAutoUpdate
                                            2759 MAU_Startup
                                              2759 mau::MAST_FindTool(__CFString const*, __CFString const*)
                                                2759 mau::FindToolInternal(short, __CFString const*, __CFString const*)
                                                  2759 FSFindFolder
                                                    2759 FindFolderGuts
                                                      2759 ResolveRelativeFolder
                                                        2759 FindFolderGuts
                                                          2759 ResolveRelativeFolder
                                                            2759 GetFolderSubFolder
                                                              2759 FSMakeFSRefUnicode
                                                                2759 PBMakeFSRefUnicodeSync
                                                                  2759 GetFSRefAttributes(FSMount*, FSRefPrivate const*, unsigned long, FSAttributeInfo*, unsigned long, char*)
                                                                    2759 FSMount::getattrs(unsigned long, char const*, unsigned long, unsigned long, FSAttributeInfo*, unsigned long, unsigned char*)
                                                                      2759 FSMount::_getattrs(unsigned long, char const*, unsigned long, unsigned long, FSAttributeInfo*, unsigned long, unsigned char*)
                                                                        2759 FSMount::getattrscore(bool, char const*, unsigned long, char const*, unsigned long, FSAttributeInfo*, unsigned long, unsigned char*)
                                                                          2759 open$UNIX2003
    2759 Thread_1503   DispatchQueue_2: com.apple.libdispatch-manager  (serial)
      2759 start_wqthread
        2759 _pthread_wqthread
          2759 _dispatch_worker_thread2
            2759 _dispatch_queue_invoke
              2759 _dispatch_mgr_invoke
                2759 kevent
    2759 Thread_2172
      2759 thread_start
        2759 _pthread_start
          2759 ExceptionHandlerThreadProc(void*)
            2759 mach_msg
              2759 mach_msg_trap
    2759 Thread_2671
      2759 thread_start
        2759 _pthread_start
          2759 PrivateMPEntryPoint
            2759 TCPListener(void*)
              2759 FWaitForConnection
                2759 accept
                  2759 accept$NOCANCEL$UNIX2003
    2759 Thread_2672
      2759 thread_start
        2759 _pthread_start
          2759 PrivateMPEntryPoint
            2759 BroadcastListener(void*)
              2759 FReceiveMessage
                2759 recvfrom
                  2759 recvfrom$NOCANCEL$UNIX2003
    2759 Thread_2673
      2759 thread_start
        2759 _pthread_start
          2759 PrivateMPEntryPoint
            2759 BroadcastSender(void*)
              2756 MPWaitOnSemaphore
                2756 semaphore_timedwait_trap
              1 FGenerateBroadcastHash(unsigned char const*, unsigned char const*, unsigned char*)
                1 FGenerateHashCore(unsigned char const*, unsigned char const*, unsigned long, unsigned char*)
                  1 BatteryCount
                    1 IOPMCopyBatteryInfo
                      1 IOServiceGetMatchingServices
                        1 io_service_get_matching_services
                          1 mach_msg
                            1 mach_msg_trap
              1 FGetMACAddress(unsigned char*)
                1 MopRcfdCopyEthernetMACAddress
                  1 IOServiceGetMatchingServices
                    1 io_service_get_matching_services
                      1 mach_msg
                        1 mach_msg_trap
              1 UsingPPP
                1 SCNetworkCheckReachabilityByAddress
                  1 SCNetworkReachabilityCreateWithAddress
                    1 __SCNetworkReachabilityCreatePrivate
                      1 _CFRuntimeCreateInstance
                        1 malloc_zone_malloc
                          1 szone_malloc_should_clear
                            1 tiny_malloc_from_free_list
Total number in stack (recursive counted multiple, when >=5):
Sort by top of stack, same collapsed (when >= 5):
        mach_msg_trap        2761
        accept$NOCANCEL$UNIX2003        2759
        kevent        2759
        open$UNIX2003        2759
        recvfrom$NOCANCEL$UNIX2003        2759
        semaphore_timedwait_trap        2756
Sample analysis of process 164 written to file /dev/stdout

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