I've ran a software agency for 8 years, and whats worked best for us is using PERT (Program Evaluation and Review Technique) estimation, or 3-point estimation,

I've ran a software agency for 8 years, and whats worked best for us is using PERT (Program Evaluation and Review Technique) estimation, or 3-point estimation, where you individually estimate optimistic, pessimistic, and most likely cases - to then calculate a weighted average. Whilst I've found this can help weed out biases and gut feelings - I still add a multiplier that i've refined over the years. Basically chaos allowance, that aims to take into account the things you can't possible take into account yet. I think me the most common cause of estimation issues arises more from unclear acceptance criteria, rather than calculation issues, so i've learn to work with my clients to capture a huge level of detail in the user story acceptance criteria (kind of anti-agile I know), and only then do a fine grained estimate for every story. This undoubtedly takes a lot of time, but in the end it's what works well on the majority of my projects (i generally do this in a paid scoping phase).