There really is no way to check if our computer is infected without running scans with protection software like Microsoft Security Essentials or Malwarebytes Antimalware. The paid version of MBAM (Malwarebytes Antimalware) has active protection that will check files as they are downloaded, but as stated it is a pay per use solution. It is the best piece of software I have personally found to check to see if files are infected when they are downloaded.
The other thing you can do is search for online scanners. These sites allow you to post a link to a file and it will check that file for you to let you know if it is safe to download. While it is an extra step, if you are looking to stay protected, this is something you could consider instead of purchasing MBAM. But other than that you really dont have any way without running a scan of some sort to know if your PC is infected.
That is the only sure fire way I know of. Being one of the few people on the site who do virus removal help, I always recommend MBAM to users when they say they have an infection. I also point them toward HiJack This. You can read tutorials online on how to use that software so you can try to teach yourself, but it is always good to have someone else read the logs it generates to know more for sure.
As far as system maintenance, aside from running clean manager to clean up unused files the only other thing I can suggest is the use of ChkDsk if you see a problem. A system disk defrag is a good idea, but few people realize that Windows Vista, Windows 7 and Windows 8 all do this by default once the system reaches a certain fragmentation percentage. So really the system is already doing this for you every so often. But some still choose to run O&O Defrag or Defraggler to defrag their drives manually. Some say these tools are a bit better than the built in Windows one, but honestly I havent had any issue with letting Windows take care of this aspect itself.
Really if you keep your system clean of temp files and make sure your not infected, your system performance should be maintained at a level that is acceptable.