I use Link Removed, Link Removed Home 2011 backup software. The UI is not friendly, but it does everything. I would like to make a side-by-side with other backup programs.
In addition to automatically making an image file of the system partition I want to make zip files of certain Applicsation Data files and installation configurations.
You can use Acronis to do this, and since you already have it, you are in the clear. Windows Backup can do it as well, but look at just creating image backups of particular folders. They do not have to be zip files per se. The Acronis backup file can be placed in a separate directory for these kinds of files, and you can use a different level of file compression in the backup settings. This will make the backup take a longer amount of time.
As far as backing up actual application data and installation configurations, this is not an easy task, as if you cannot restore a system image after a failure, what is going to happen here is you may want to think "Well, I still have the installation configuration and App Data. I should be fine." This is not always the case: As you may know, the registry is going to be completely different with a clean install if your image restore fails.
If you want to backup certain files that don't take up much space, look at the 2GB of free space that comes with Dropbox and even more space with Windows Live Skydrive. These are cloud-based file backup solutions.
Ultimately, though, why not just make a scheduled task in Acronis to backup individual files and folders using maximum compression (least amount of space but longest backup time)? This will spare you from using multiple programs to accomplish the same task.
All of the extra processes you are using to clean up your PC will compound your problem by adding too many variables. If you want everything to run on auto-pilot, you should consider just creating full image backups of your system in Acronis. I don't bother with incremental or differential backups with the software, because the chance for error in restoring the backup becomes exponentially greater each time an incremental or differential backup is made. The best bet, if you have enough space, is to keep doing full backups. Just say you do a full backup of everything, correct? You have an image of the System Reserve, the C drive, and any additional drives on the computer. Well, you can still use Acronis to go back into the image file and only restore certain files you want.
Having any full image backup is better than none at all - preserving these extra application data files and so forth would just be redundant form of backup - if stored on the same source it is almost entirely pointless. If the backup drive fails, you lose the images and the double backup of application data you made.
Try to simplify the process and accept that if the system goes down, you have full recourse to go back in time.
You are dealing with multiple issues. With malware and anti-virus, what were you using before? Check out my AV Comparatives post in this debate:
Link Removed