While some stations maybe will make pre-transitions some 3.000 wont make it at all. The cost to buy the equipment needed for digital broadcasts exceeds the budget for many small stations that made the investment once for analog broadcasts. Because of the mandatory transition in 2009 they now operate under different rules that excludes them from the actual DTV transition. U.S News Tech writer David La Gesse wrote some time ago at Daves Download on the subject that has been on FCCs mind for a long time. (When I met FCC last year they talked about the situation for small TV stations).
But for consumers the issue will trickle down in a slow motion. When they notice that it wont be that easy to view the local religious or civic channel that they are used to watch. Maybe the web (IPTV) can be a new outlet for niche TV?
What you can do:
If you are watching a small TV station with niched local programming, check their website or call them and ask how and if they are planning to switch to digital. If not, you will need to find a converter box that let the analog signal trough to the TV set alongside with the digital signal. In that way you will be able to switch between digital or analog signal or if you put the box on stand-by the analog signal should be able to still work on your TV set.
If you plan to buy a new digital TV set explain the situation for the retailer and let them guide you to the right equipment.