Your logs are clean essentially. That Windows Messenger that you say you have disabled in Services but IS still running, when you look in Services does it show that it is Stopped? If not, Stop it.

You do have a lot of unnecessary items running at Start Up which can be disabled using a program like the FREE Mike Lin's StartUp Control Panel
Very simple, easy to use to control items which are not needed to run at start and all can easily be run manually.
Here is a list of items, and explanation of what they are, showing in your HJT log which you don't need running all the time;

O4 - HKLM\..\Run: [PaperPort PTD] "C:\Program Files\Scansoft\PaperPort\pptd40nt.exe"
"PaperPort" software associated with scanners

O4 - HKLM\..\Run: [NvCplDaemon] "RUNDLL32.EXE" C:\WINDOWS\system32\NvCpl.dll,NvStartup
System Tray icon used to change display settings, change the clock rate and memory speed for nVidia based graphics cards. This is unnecessary since you can easily configure these settings the way you want them in the Display Properties and not have to mess with them again. Also disable the "NVIDIA Driver Helper Service" if enabled as it can cause this entry to be re-enabled on re-boot (note that this service can also cause extreme shutdown delays if enabled

O4 - HKLM\..\Run: [NvCplDaemon] "RUNDLL32.EXE" C:\WINDOWS\system32\NvCpl.dll,NvStartup
NeroCheck
Associated with "Nero Burning Rom" CD writing software. Checks for driver issues

O4 - HKLM\..\Run: [Microsoft Works Update Detection] "C:\Program Files\Microsoft Works\WkDetect.exe"
Checks for updates to MS Works

O4 - HKLM\..\Run: [Microsoft Works Portfolio] "C:\Program Files\Microsoft Works\WksSb.exe" /AllUsers
Works Portfolio tool lets you collect and organize text and pictures from the Web or your favorite program.Can be prevented from starting from a setting within Portfolio

O4 - HKLM\..\Run: [IndexSearch] "C:\Program Files\Scansoft\PaperPort\IndexSearch.exe"
Associated with PaperPort scanner software from ScanSoft

O4 - HKLM\..\Run: [FastUser] C:\WINDOWS\System32\fast.exe
Installs as part of Windows XP PowerToys as an option for very-fast user switching (allowing a keystoke to switch users instead of using the login screen). It is only used for the hot-key switch and yet it hogs 1.5 megs of memory in two separate processes (one run by the user & one by the system). Optional install in PowerToys

O4 - HKLM\..\Run: [CoolSwitch] C:\WINDOWS\System32\taskswitch.exe
ALT TAB replacement Powertoy for Windows XP - enhances the graphics displayed when you want to switch between programs running full-screen

O4 - HKLM\..\Run: [BackgroundSwitcher] C:\WINDOWS\System32\bgswitch.exe
Background Switcher Powertoy. Included with the last beta version of the XP Powertoys. Whenever a user right clicked his desktop and chose properties he could see a new tab which allowed him to enable a "Desktop Slide Show." This would automatically change the Windows Desktop at an interval specified by the user.

O4 - HKLM\..\Run: [RoxWatchTray] "C:\Program Files\Common Files\Roxio Shared\9.0\SharedCOM
\RoxWatchTray9.exe"
Related to Roxio_easy_CD_creater System Tray icon installed by Roxio Easy Media Creator 8 and which allows you to configure your watched folders or to turn the Watched Folders feature of Roxio ON or OFF. Note: located in C:\Program Files\Common Files\Roxio Shared\...

O4 - HKLM\..\Run: [DMXLauncher] "C:\Program Files\Roxio\Media Experience\DMXLauncher.exe"
Part of Dell's Media Experience, a multimedia suite which offers the user functionality to organise and play music and digital video files.

O4 - HKLM\..\Run: [RoxioDragToDisc] "C:\Program Files\Roxio\Drag-to-Disc\DrgToDsc.exe"
Part of Roxio EasyCD Creator 6.0 - places the Roxio Drag-to-Disc icon in you system tray. "Easily drag and drop files for burning to CD or DVD. Disc formatting and burning will happen automatically". Not required for Roxio to work properly

O4 - HKLM\..\Run: [NvMediaCenter] "RUNDLL32.EXE" C:\WINDOWS\system32\NvMcTray.dll,NvTaskbarInit
System Tray icon used to manage settings for nVidia based graphics cards. May be required for some 3D applications to recognize your card correctly - such as the game "Everquest". Otherwise, settings can be changed manually via Display Properties

O4 - HKLM\..\Run: [QuickTime Task] "C:\Program Files\QuickTime\qttask.exe" -atboottime
System Tray access to Apple's "Quick Time" viewer from version 5 onwards

O4 - HKLM\..\Run: [iTunesHelper] "C:\Program Files\iTunes\iTunesHelper.exe"
Installed with Apple's iTunes for Windows. Uses ~3-4MB of memory and if disabled in MSCONFIG or deleted from the registry it will re-instate itself after running iTunes a few times

O4 - HKLM\..\Run: [ISUSPM Startup] "C:\PROGRA~1\COMMON~1\INSTAL~1\UPDATE~1\ISUSPM.exe " -startup
InstallShield Update Service related; Automatically searches for and performs any updates to the software. Not required.

O4 - HKLM\..\Run: [ISUSScheduler] "C:\Program Files\Common Files\InstallShield\UpdateService\issch.exe" -start
InstallShield Update Service Scheduler; automatically searches for and performs any updates to the software so you’re always working with the most current version. Not required.

O4 - HKLM\..\Run: [SunJavaUpdateSched] "C:\Program Files\Java\jre1.5.0_11\bin\jusched.exe"
Checks with Sun's Java updates site to see if newer Java versions are available. Visit http://java.sun.com or just run the Java Plug-In Control Panel

O4 - Global Startup: Microsoft Office.lnk = C:\Program Files\Microsoft Office\Office10\OSA.EXE
Auto Start for Microsoft Office can easily be run manually. It's somewhat of a resource hog

O4 - Global Startup: Adobe Reader Speed Launch.lnk = C:\Program Files\Adobe\Acrobat 7.0\Reader\reader_sl.exe
Quick launch for Adobe Reader. Not required and can easily be run manually.

O4 - Global Startup: Microsoft Works Calendar Reminders.lnk = C:\Program Files\Common Files\Microsoft Shared\Works Shared\
Produces a pop-up reminder of events scheduled using the MS Works Calendar

Now these are all user choice on whether you want them to run at start up and with many of them, all the time. They all can be run manually.