What instructional design methodology do you prefer to use for your organisation and projects and why do you choose it over others?

There is no definite solution. You can choose to mix the best of multiple models to suit your requirements. 

Because I have large number of stakeholders and execute multiple projects simultaneously, I use a hybrid model that includes ADDIE and Agile model. This helps me to keep the all stakeholder connected to the training goals as well as show progress on multiple fronts to ensure that projects are progressing towards completion. This model also ensures that there are very less scope creeps and any delays are escalated in a timely mannger