In reply to your last comment to my answer, I think most would agree there's not enough information to provide a precise solution for you.
Reinstalling .NET was an educated guess, but we can't know what other files/registry entries your clean-up utilities deleted, and which one might have been critical.
My first answer is: If reinstalling the application doesn't help, contact your vendor/developer to figure it out. The vendor knows what files are expected upon launching their application, we don't!
Then I noticed in your profile you posted a question on stackoverflow where you indicate that your C drive "hardly have any kb left" - which probably initiated your clean-up. Well, you know, that would be the first thing I'd try to fix if I were you. You should make sure to always have at least 1 GB free.
A few MB free space is asking for troubles and could certainly cause "need to close" errors if space attempts to be allocated by windows or your applications. Also it would help avoiding the need for extreme clean-ups and inadvertently delete important files.
Thus my second answer is: Get a new (or use another) bigger main hard drive ASAP. If your applications still crash, you may need to reinstall Windows and all applications/drivers on it. It's a lot of work, but it's ultimately an excellent solution to your problem (read: it will almost certainly fix it).
Finally, clean-up utilities aren't official utilities. It's true that Windows tend to accumulate stuff, but that clean-up utilities do a good job at stripping it down is debatable. Most of Windows growth is from libraries (DLLs), and updates and various installed applications, which utilities should not attempt to mess with too much anyway. Temporary folders are easy to clean-up by hand from time to time. Often the best clean-up you can do is uninstalling applications you don't absolutely require. You know, I find most clean-up tools add more bloat than whatever they clean. That huge list of anti-malware you have installed also seems overkill for the job at hand.
So my third answer is: Go easy on cleaning-up in the future. Disk space is cheap enough that you should be able to avoid all this trouble to save a few megabytes.
Favor uninstalling unused applications, and delete "TEMP" folders by hand from time to time. As much as possible, avoid installing many applications just to try them - as this contributes to needless windows growth that's hard to get back. Ideally, stick to one good anti-virus, one good anti-malware, and whatever you need to work. Avoid messing with the registry!
6What application? – BBlake – 2012-02-25T15:40:17.150
6They aren't actually sorry. – Daniel Beck – 2012-02-25T16:05:06.220
4Note that registry cleaners (step 2) are more likely to cause problems than to solve them. – Harry Johnston – 2012-02-28T02:46:47.417
In addition to @BBlakes's comment, is it a legal one? – cutrightjm – 2012-05-09T16:43:28.353
What kind of application is it? Win32, .Net? If it's not .Net, .Net Framework has nothing to do with it. – None – 2012-05-10T12:57:36.057