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I have recently fixed two PCs where the owner has installed huge numbers of (mainly free) programs. In itself this is not a problem, but the more programs that are installed the greater the chance of one unintentionally messing with another - either when they are installed or as a result of them both residing in memory. Moreover, rectifying unrelated faults often takes more time, and therefore cost, as not only is more testing than usual at the end of a repair required, but there is a greater propensity for configuration changes that adversely affect a program.
The more programs that are installed in memory the slower the PC performs generally as they all compete for a slice of the limited memory resource. Not only that but as increased paging is required, there is a greater risk that program faults will develop when shutting down a computer that is completing maintenance operations in the background.
In general, but especially in the above cases, I recommend having CPU and disk activity meters permanently visible on the desktop. These are freely available, for example as gadgets from Microsoft or Google
This will enable you to postpone significant events (e.g. program (un)installation, shutting down the computer, calling for support when something is not working as expected) until the PC is quiesced - hence, limiting the likelihood of interrupting an important modification to the system state.
In much the same vein, it is good to let the system finish its start up procedures as much as possible before beginning work. So start the computer 5 minutes before you start work and shut down 5 minutes after you close the last program to reduce the risk of interrupting important background tasks.
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