Unable to open any of my applications

I am no longer able to open any of my applications on my desk top. This problem has only just occured now. Seems to have happened when I was trying to remove some spyware from my computer, but when I try to open something i.e. music, the window frame appears but the little power bar on top of the window grows slower and slower the more it loads and never seems to reach the end. Is it somthing to do with removing the trojan? Is the trojan still there? Or did I accidentally delete a necessary file somewhere along the line. Please help! Thanks in advance