your concern is valid...too much cleaning is more harmfull then helpfull
for instance, registry cleaners will usually recognize as invalid some entries that you will miss in the future, and you won't even recognize the problem when it arises
spybot can easily remove some very functiional history logs...history, address completion, stuff that I use every day
adaware will rmove some keys on programs and render them invalid, where you might have prefered to keep using the program...like dap, or eudora...though eudora is no longer a target, it will be again soon