It's effectively impossible to compare two programming projects, as there are too many factors that mean that the metrics from only aren't applicable to another (e.g., specific technologies used, prior experience of the developers, shifting requirements). Unless you are stamping out another system that is almost identical to one you've built previously, your estimates are going to have a low probability of being accurate.
A caveat is when you're building the next revision of an existing system with the same team; the specific experience gained does improve the ability to estimate the next batch of work.
I've seen too many attempts at estimation methodology, and none have worked. They may have a pseudo-scientific allure, but they just don't work in practice.
The only meaningful answer is the relatively short iteration, as advocated by agile advocates: choose a scope of work that can be executed within a short timeframe, deliver it, and then go for the next round. Budgets are then allocated on a short-term basis, with the stakeholders able to evaluate whether their money is being effectively spent. If it's taking too long to get anywhere, they can ditch the project.