Aye. The example of Prezi is apt here too. Using Prezi changed how I thought of slideshows, and as a result my presentations had more movement and interactivity than before.
Agenda made me realize how iterative note taking should be, and reified the link between notes, projects, and future events on the calendar.
DEVONthink convinced me to take long-term personal knowledge management more seriously. It also made permanent, cross-platform/device file locations more important.
I don’t use Prezi or Agenda anymore, but I like letting the tools shape me a little!