What happens when you try to download something? Have you tried the Right Click > Save Target AS method?
One thing you can try is to go to Start>Run, enter
msconfig and temporarily disable the "startup" group on the General page to eliminate any current conflicts. Then see if you can download, install, update and run Spybot
Free Scratch and Win should not be preventing a download so you may have other problems as well. But try the method I suggested.
Also if you could manage to get a copy of StartupList.exe and run and copy/paste the results of that, before disabling the startup group, that might be very helpful in further diagnosis.
http://www.lurkhere.com/~nicefiles/
If you can't do that, try this: Start>Run, enter
msinfo32 and then click Software Environment > Startup Programs. Then click Edit>Select All>Edit>Copy and paste the copied text here. This must be done before using msconfig.
>>Also, are you able to run the IE Repair Tool usually found by going to Add/Remove Programs > Internet Explorer > Repair > Remove ?