Why do this, since even stock plans cost you at least a couple of hundred dollars each? Because the right stock plans can save you tons of time and money if you have a talented architect. Most plans are at least partly modular these days, and often you can even order prefabricated sections pegged to a specific house plan.
Drawing a good set of custom home plans involves integrating many different concepts and ideas into a solid and usable working plan. Many designers are able to come up with a unique or interesting preliminary design, but fail to deliver when its time to detail the house structure. They draw a pretty picture but have little or no understanding of how to translate that nice design into a working plan which the builder can understand.
Remember that plans are not necessarily "as is." Builders can use a reverse set of plans (sometimes called a mirror image) to better site a house. It's also possible to hire an architect or modification service to personalize a plan. Ask if reproducible prints or electronic CADD files are available for the selected plan. Either will make the alteration process quicker and easier.
Another item which is often missing or lacking in a set of house plans is comprehensive and accurate dimensions. We have always strived to provide more than the minimum amount of house dimensions so that it is easy for the owner and builder to layout a home on its building site. We will even calculate point to point dimensions (using trigonometry) for homes which have lots of odd angles to them (as opposed to a simple rectangle layout). Not all architects or designers will go this "extra mile," so it pays to check these things out beforehand.