SunDevil, I think you are correct that these are organized by division. But I can't figure out the pattern within the divisions (if there is one). Alphabetical by player name or team name would make sense, but doesn't seem to apply here, nor does final standings within the year. Do we have a checklist for the 2008 set as a reference? That might help figure out what they were doing.
C2Cigars, I can see your point for some situations. For example, I have a single oddball card from a minor league team set that I think was issued at a minor league game. No idea how many cards are in the set, nor do I know the other players in the set. In this case, I would argue it would be a "useless" checklist since too much info would be unknown.
In this 2006 Upper Deck DC case, we are reasonably confident that we know many cards are in the set and which cards they are. We ever know a few numbers. As a user, is it way more useful to have a "work-in-progress" checklist than to have nothing at all. I'm new here, but isn't this the same logic that allows image scans to be added for some cards in a set. Do we need to wait until every card in a set has an image before any card can be added with an image? Are these images useless because they are not available for the entire set? No, because some information >> no information.
Finally, here is the running list of this of what we know:
DC-20 Albert Pujols St Louis Cardinals NL Central
DC-21 Derrek Lee Chicago Cubs NL Central
DC-25 Ken Griffey, Jr. Cincinnati Reds NL Central
DC-28 Chase Utley Philadelphia Philies NL East
Other NL Central Players from the year would fit the pattern noted by SunDevil, as would the DC-28 Utley.
DC-? (22,23,24) Jason Bay Pittsburgh Pirates
DC-? (22,23,24) Ben Sheets Milwaukee Brewers
DC-? (22,23,24) Craig Biggio Houston Astros