All these ideas that people are listing (isolation, least privilege, white-listing) are tools.
But you first have to know what "security" means for your application. Often it means something like
- Availability: The program will not fail to serve one client because another client submitted bad data.
- Privacy: The program will not leak one user's data to another user
- Isolation: The program will not interact with data the user did not intend it to.
- Reviewability: The program obviously functions correctly -- a desirable property of a vote counter.
- Trusted Path: The user knows which entity they are interacting with.
Once you know what security means for your application, then you can start designing around that.
One design practice that doesn't get mentioned as often as it should is Object Capabilities.
Many secure systems need to make authorizing decisions -- should this piece of code be able to access this file or open a socket to that machine.
Access Control Lists are one way to do that -- specify the files that can be accessed. Such systems though require a lot of maintenance overhead. They work for security agencies where people have clearances, and they work for databases where the company deploying the database hires a DB admin. But they work poorly for secure end-user software since the user often has neither the skills nor the inclination to keep lists up to date.
Object Capabilities solve this problem by piggy-backing access decisions on object references -- by using all the work that programmers already do in well-designed object-oriented systems to minimize the amount of authority any individual piece of code has. See CapDesk for an example of how this works in practice.
DARPA ran a secure systems design experiment called the DARPA Browser project which found that a system designed this way -- although it had the same rate of bugs as other Object Oriented systems -- had a far lower rate of exploitable vulnerabilities. Since the designers followed POLA using object capabilities, it was much harder for attackers to find a way to use a bug to compromise the system.