I've been trying to clean up whilst I await your response.
Been reading some more and using the proggies and processes you guys ask for. Anyway I seem to have got rid of all the pop-ups and am now getting a clean scan with Spybot, Ad-aware, and McAfee.
One thing I haven't done is fix any findings from HJT as I don't have a clue. I hope I haven't screwed anything up so here is an updated HJT log. Please advise on anything else.

Logfile of Trend Micro HijackThis v2.0.0 (BETA)
Scan saved at 11:22:18 PM, on 6/9/2007
Platform: Windows XP SP2 (WinNT 5.01.2600)
Boot mode: Normal

Running processes:
C:\WINDOWS\System32\smss.exe
C:\WINDOWS\system32\winlogon.exe
C:\WINDOWS\system32\services.exe
C:\WINDOWS\system32\lsass.exe
C:\WINDOWS\system32\Ati2evxx.exe
C:\WINDOWS\system32\svchost.exe
C:\WINDOWS\System32\svchost.exe
C:\WINDOWS\system32\Ati2evxx.exe
C:\WINDOWS\system32\spoolsv.exe
C:\WINDOWS\Explorer.EXE
C:\WINDOWS\system32\VTTimer.exe
C:\WINDOWS\SOUNDMAN.EXE
C:\WINDOWS\system32\devldr32.exe
C:\WINDOWS\system32\ctfmon.exe
C:\PROGRA~1\Lavasoft\AD-AWA~2\Ad-Watch.exe
C:\Program Files\Logitech\SetPoint\KEM.exe
C:\Program Files\Logitech\SetPoint\KHALMNPR.EXE
C:\Program Files\Common Files\McAfee\HackerWatch\HWAPI.exe
C:\PROGRA~1\McAfee\MSC\mcmscsvc.exe
c:\program files\common files\mcafee\mna\mcnasvc.exe
C:\PROGRA~1\McAfee\VIRUSS~1\mcods.exe
C:\PROGRA~1\McAfee\MSC\mcpromgr.exe
c:\PROGRA~1\COMMON~1\mcafee\mcproxy\mcproxy.exe
c:\PROGRA~1\COMMON~1\mcafee\redirsvc\redirsvc.exe
C:\PROGRA~1\McAfee\VIRUSS~1\mcshield.exe
C:\PROGRA~1\McAfee\VIRUSS~1\mcsysmon.exe
C:\Program Files\McAfee\MPF\MPFSrv.exe
C:\PROGRA~1\McAfee\MPS\mps.exe
C:\WINDOWS\system32\MsPMSPSv.exe
c:\PROGRA~1\mcafee.com\agent\mcagent.exe
C:\Program Files\McAfee\MPS\mpsevh.exe
c:\PROGRA~1\mcafee\VIRUSS~1\mcvsshld.exe
C:\WINDOWS\system32\wuauclt.exe
C:\Program Files\HiJackThis_v2\Scanner.exe

R0 - HKCU\Software\Microsoft\Internet Explorer\Main,Start Page = http://uk.yahoo.com/
R1 - HKLM\Software\Microsoft\Internet Explorer\Main,Default_Page_URL = http://go.microsoft.com/fwlink/?LinkId=69157
R1 - HKLM\Software\Microsoft\Internet Explorer\Main,Default_Search_URL = http://go.microsoft.com/fwlink/?LinkId=54896
R1 - HKLM\Software\Microsoft\Internet Explorer\Main,Search Page = http://go.microsoft.com/fwlink/?LinkId=54896
R0 - HKLM\Software\Microsoft\Internet Explorer\Main,Start Page = http://go.microsoft.com/fwlink/?LinkId=69157
R1 - HKCU\Software\Microsoft\Windows\CurrentVersion\Internet Settings,ProxyServer = 80.50.82.90:80
R1 - HKCU\Software\Microsoft\Windows\CurrentVersion\Internet Settings,ProxyOverride = localhost
O2 - BHO: Adobe PDF Reader Link Helper - {06849E9F-C8D7-4D59-B87D-784B7D6BE0B3} - C:\Program Files\Adobe\Acrobat 7.0\ActiveX\AcroIEHelper.dll
O2 - BHO: (no name) - {18A04AEE-2F62-4929-A047-A17B08AA367c} - (no file)
O2 - BHO: (no name) - {53707962-6F74-2D53-2644-206D7942484F} - C:\PROGRA~1\SPYBOT~1\SDHelper.dll
O2 - BHO: (no name) - {5F771C95-544B-4E9E-AC5D-F4E49C7F9662} - (no file)
O2 - BHO: (no name) - {6A0D10D3-3D3B-4067-ADB8-F1B603916D43} - (no file)
O2 - BHO: SSVHelper Class - {761497BB-D6F0-462C-B6EB-D4DAF1D92D43} - C:\Program Files\Java\jre1.6.0_01\bin\ssv.dll
O2 - BHO: scriptproxy - {7DB2D5A0-7241-4E79-B68D-6309F01C5231} - c:\program files\mcafee\virusscan\scriptcl.dll
O2 - BHO: (no name) - {92A444D2-F945-4dd9-89A1-896A6C2D8D22} - (no file)
O2 - BHO: (no name) - {AC443AAB-CE0D-4F42-B10F-F1AFA04F5604} - (no file)
O2 - BHO: (no name) - {CA1BBD12-DDB9-479F-906E-4E55C2E15604} - (no file)
O4 - HKLM\..\Run: [VTTimer] VTTimer.exe
O4 - HKLM\..\Run: [VTTrayp] VTtrayp.exe
O4 - HKLM\..\Run: [SoundMan] SOUNDMAN.EXE
O4 - HKLM\..\Run: [RemoteControl] C:\Program Files\Roxio\Roxio DVDMax Player\PDVDServ.exe
O4 - HKLM\..\Run: [SunJavaUpdateSched] "C:\Program Files\Java\jre1.5.0_11\bin\jusched.exe"
O4 - HKCU\..\Run: [ctfmon.exe] C:\WINDOWS\system32\ctfmon.exe
O4 - HKCU\..\Run: [AWMON] "C:\PROGRA~1\Lavasoft\AD-AWA~2\Ad-Watch.exe"
O4 - Global Startup: Logitech SetPoint.lnk = C:\Program Files\Logitech\SetPoint\KEM.exe
O8 - Extra context menu item: E&xport to Microsoft Excel - res://C:\PROGRA~1\MICROS~3\Office12\EXCEL.EXE/3000
O9 - Extra button: (no name) - {08B0E5C0-4FCB-11CF-AAA5-00401C608501} - C:\Program Files\Java\jre1.6.0_01\bin\ssv.dll
O9 - Extra 'Tools' menuitem: Sun Java Console - {08B0E5C0-4FCB-11CF-AAA5-00401C608501} - C:\Program Files\Java\jre1.6.0_01\bin\ssv.dll
O9 - Extra button: Send to OneNote - {2670000A-7350-4f3c-8081-5663EE0C6C49} - C:\PROGRA~1\MICROS~3\Office12\ONBttnIE.dll
O9 - Extra 'Tools' menuitem: S&end to OneNote - {2670000A-7350-4f3c-8081-5663EE0C6C49} - C:\PROGRA~1\MICROS~3\Office12\ONBttnIE.dll
O9 - Extra button: Research - {92780B25-18CC-41C8-B9BE-3C9C571A8263} - C:\PROGRA~1\MICROS~3\Office12\REFIEBAR.DLL
O9 - Extra button: (no name) - {e2e2dd38-d088-4134-82b7-f2ba38496583} - %windir%\Network Diagnostic\xpnetdiag.exe (file missing)
O9 - Extra 'Tools' menuitem: @xpsp3res.dll,-20001 - {e2e2dd38-d088-4134-82b7-f2ba38496583} - %windir%\Network Diagnostic\xpnetdiag.exe (file missing)
O9 - Extra button: Messenger - {FB5F1910-F110-11d2-BB9E-00C04F795683} - C:\Program Files\Messenger\msmsgs.exe
O9 - Extra 'Tools' menuitem: Windows Messenger - {FB5F1910-F110-11d2-BB9E-00C04F795683} - C:\Program Files\Messenger\msmsgs.exe
O16 - DPF: {0EB0E74A-2A76-4AB3-A7FB-9BD8C29F7F75} (CKAVWebScan Object) - http://www.kaspersky.com/kos/english...an_unicode.cab
O16 - DPF: {17492023-C23A-453E-A040-C7C580BBF700} (Windows Genuine Advantage Validation Tool) - http://go.microsoft.com/fwlink/?linkid=39204
O16 - DPF: {193C772A-87BE-4B19-A7BB-445B226FE9A1} (ewidoOnlineScan Control) - http://downloads.ewido.net/ewidoOnlineScan.cab
O18 - Protocol: skype4com - {FFC8B962-9B40-4DFF-9458-1830C7DD7F5D} - C:\PROGRA~1\COMMON~1\Skype\SKYPE4~1.DLL
O20 - Winlogon Notify: awtsq - C:\WINDOWS\system32\awtsq.dll (file missing)
O20 - Winlogon Notify: ddccy - C:\WINDOWS\system32\ddccy.dll (file missing)
O20 - Winlogon Notify: gebcb - C:\WINDOWS\system32\gebcb.dll (file missing)
O20 - Winlogon Notify: gebyx - C:\WINDOWS\system32\gebyx.dll (file missing)
O22 - SharedTaskScheduler: Browseui preloader - {438755C2-A8BA-11D1-B96B-00A0C90312E1} - C:\WINDOWS\system32\browseui.dll
O22 - SharedTaskScheduler: Component Categories cache daemon - {8C7461EF-2B13-11d2-BE35-3078302C2030} - C:\WINDOWS\system32\browseui.dll
O23 - Service: Ati HotKey Poller - ATI Technologies Inc. - C:\WINDOWS\system32\Ati2evxx.exe
O23 - Service: McAfee E-mail Proxy (Emproxy) - McAfee, Inc. - C:\PROGRA~1\COMMON~1\McAfee\EmProxy\emproxy.exe
O23 - Service: InstallDriver Table Manager (IDriverT) - Macrovision Corporation - C:\Program Files\Common Files\InstallShield\Driver\1050\Intel 32\IDriverT.exe
O23 - Service: McAfee HackerWatch Service - McAfee, Inc. - C:\Program Files\Common Files\McAfee\HackerWatch\HWAPI.exe
O23 - Service: McAfee Update Manager (mcmispupdmgr) - McAfee, Inc. - C:\PROGRA~1\McAfee\MSC\mcupdmgr.exe
O23 - Service: McAfee Services (mcmscsvc) - McAfee, Inc. - C:\PROGRA~1\McAfee\MSC\mcmscsvc.exe
O23 - Service: McAfee Network Agent (McNASvc) - McAfee, Inc. - c:\program files\common files\mcafee\mna\mcnasvc.exe
O23 - Service: McAfee Scanner (McODS) - McAfee, Inc. - C:\PROGRA~1\McAfee\VIRUSS~1\mcods.exe
O23 - Service: McAfee Protection Manager (mcpromgr) - McAfee, Inc. - C:\PROGRA~1\McAfee\MSC\mcpromgr.exe
O23 - Service: McAfee Proxy Service (McProxy) - McAfee, Inc. - c:\PROGRA~1\COMMON~1\mcafee\mcproxy\mcproxy.exe
O23 - Service: McAfee Redirector Service (McRedirector) - McAfee, Inc. - c:\PROGRA~1\COMMON~1\mcafee\redirsvc\redirsvc.exe
O23 - Service: McAfee Real-time Scanner (McShield) - McAfee, Inc. - C:\PROGRA~1\McAfee\VIRUSS~1\mcshield.exe
O23 - Service: McAfee SystemGuards (McSysmon) - McAfee, Inc. - C:\PROGRA~1\McAfee\VIRUSS~1\mcsysmon.exe
O23 - Service: McAfee Personal Firewall Service (MpfService) - McAfee, Inc. - C:\Program Files\McAfee\MPF\MPFSrv.exe
O23 - Service: McAfee Privacy Service (MPS9) - McAfee, Inc. - C:\PROGRA~1\McAfee\MPS\mps.exe
O23 - Service: NBService - Nero AG - C:\Program Files\Nero\Nero 7\Nero BackItUp\NBService.exe

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