This is an excellent although slightly outdated guide.
First thing you should do – check what your warranty allows you to do. Then check if the components in your pc are compatible with retail ones (power connectors, MB mounting sockets, etc)
Second, Locate the source of noise.
Case fans: Easy to replace and mount. Just take any silent 3 pin or 4 pin on the market with the desired size and replace. Keep the airflow direction the same. Slow 120 mm fans have amazing airflow while very quiet. Vibration absorbing pads are welcome.
CPU fan: Again the market is saturated with high quality and performance coolers. If your MB is standard and has the proper mounting holes just buy the one that best fits in your budget and noise requirements. Vibration absorbing pads are welcome.
PSU fan: Don't know here. It could be replaceable but there will be some (dis)assembly required. Otherwise - replace the PSU – again a lot of excellent choices on the market.
VGA cooler: There are aftermarket solutions, but I cannot comment – usually when my vga shrieks a lot, I cannot hear it because of the sounds the zombies make when chainsawed.
Hard drives: Using SSD for a system drive and some normal hard drives for slow media data is very quiet solution, although expensive. There are also noise dampening solutions for hard drives.
Case: it could emit sounds if the case is of very poor build quality or has some loose screws, dust or cables chaffing fans.
Edit: One of the best sources for everything quiet.