Mostly when we install a system for a client will have specific needs are that outside of what the standard system can delivery. Sometimes these needs a minor, either removing or adding in some extra data or displaying a report in a different format that what we would normally deal with. Other times these changes have an effect on how the system processes transactions and are more wide spread.
One such change that we have made recently was for a Custom Manufacturing site that wanted the structure of the Bill of Materials system but also the flexibility to have optional items in his BOM easily swapped in and out. I will have a profile of this system up on the website shortly that will show some of what we achieved in this change.