Your brokerage may track this for you already. Ameritrade has a detailed cost basis tracker, and distributes the basis reduction for each nondividend distribution across all share lots held at the time of the distribution, as DianeW777 described it. Thus when you sell any shares, Ameritrade will properly report the reduced basis accordingly. In fact, Ameritrade even shows you the history per lot, so you can see each basis reduction for each lot.
Also note that Quicken uses the same strategy, if you recategorize the appropriate portion of your dividends as "Return of Capital" transactions.
