A proprietary computer is a computer that has parts in it that are meant only to be available from one retailer or manufacturer. Most people take the word proprietary to mean IBM, Compaq, and others. This is technically not right. Every notebook is proprietary in some fashion. Some computers are proprietary, but barely. Some computers are 100% proprietary. Telling the difference is important.
Proprietary computers have parts in them that are only meant to be replaced by a manufacturer's replacement part. For example, Compaq motherboards can only be replaced by Compaq motherboards, unless you want to replace the video card, sound card, and other pieces of the computer at the same time.

Custom-built computers do not have this problem. If a year from now you want a new video card, you buy a new video card and put it in the computer. All the parts are interchangeable, from the motherboard right down to the screws that close the case. They are meant to last, and if you start having problems you take out the problem and replace it. In terms of upgradeability, this is no contest. Custom built computers save you big upgrading money later on.

Computer stores that build custom computers tend to have a bad reputation. This is because they are small, and go out of business fairly easily. Running a computer store is frustrating, especially when you are in a highly competitive market. The sad fact is that 50% of computer stores that open close within 2 years.

http://www.comp-solve.com/Proprietary.htm