Over the years I have noticed that the following points help in arriving at a decision when choosing between a custom built versus pre built content management system.

1. What is the time frame in which you are required to get the site up and running?
I know, everybody wants it as of yesterday but the question here is -"Is the time frame in which the site needs to be up really critical?" Maybe you have an upcoming event before which you would like your site to online.

2. What is your budget?
Generally, the custom build would cost you more to get up and running versus going in for a pre built or existing content management system.
But, it might work out more cost effective to go in for a custom built solution in cases where the existing CMS is not very close to your needs hence even though you might be able to get your site up and running very quickly but it might cost you more down the line to customize it for your needs.
So you need to make a call.

3. Is a pre built CMS available out there which meets 80% of your requirements? ?
Let's apply the 80 - 20 rule here.
This will make sure that most of requirements are met quite quickly and your online business starts.
You can take a look at the article by me Top Five things to know when choosing an open source Content Management System (CMS).

4. What is most important aspect(s) for the site success - Time to market, user interface, usability, ease of use, performance?
You need to list down the most important factors which will define the success of your web site for your target audience or users.
Say that you are running an ecommerce site so easy of use and performance of your site is very important so that the users can quickly find what they are looking for.
If you are trying to create a web site to coincide with the launch of your product then the time to market is most important.
The computer literacy level of the users who are going to be using the content management system to create content on the site, maintain it or use it.
If the majority of the users are business people then the user friendliness of the CMS is very important whereas if your users are going to be programmers then the user interface might not be that important for them.
Clarity on this aspect will help you choose whether you need to go in for a custom built solution or a pre-built solution.

5. Can the existing pre built content management system be customized?
Can the existing pre built CMS be customized easily? Are there programmers available out there who can help you customize it? Are design services, templates available which will help you get the look and feel for the site as desired by you?
6. Who are the users who are going to be using the content management system and maintain your site?
What is the computer literacy level of the users who are going to be using the content management system to create content on the site, maintain it or use it.
If the majority of the users are business people then the user friendliness of the CMS is very important whereas if your users are going to be programmers then the user interface might not be that important for them.

7. Do you have a technology preference?
You might prefer a particular technology maybe because you already have other applications running on that technology which you would like to integrate with the content management system you are trying to build or use.

The above points will not only help you in deciding between a custom built and pre-built content management system but they are equally true for choosing between customized software development or off the shelf solution.