Last place I worked used DataJunction for the print service bureau side of the business (e.g., bank check printing, etc). While what DJ does is cool, it does store the "design" in a binary file format. It would be nice if it was XML or other similar text-based file. Why's that? Well, one of the weaknesses we noted is that it doesn't really do templates, so it's up to the people using it to have any standardization for creating mapping files. When you have multiple people working on different import packages for files, then it seems no one does it in a standard, repeatable (and, because of the binary DJ files, discoverable) fashion. One customer's address data might go in fields1-5 (literally), and another might be fields10-15...
I had a crazy project there where it would have been nice to be able to scan over the DJ packages to figure out where it mapped data into the generic table structure in the database for each customer, but had to talk to DJ devs to dig out the data mapping for each customer.
As far as what DJ does, it's...better...than SSIS for this kind of work.