If you were running a gaming system getting a matched pair of 1gb dimms with fast timings would be ideal. Memory like that however will generally see a higher price over the usual performance and value memory available. For a system where you plan on having more then one program running the dual channel mode offers the first channel for the active programs while background services for Windows and minimized programs should be forced to use the secondary.
When the first dimm is smaller the amount of memory used it fills up first causing a bleedover to the next dimm. This can cause problems known as "memory holes". When running high end games or large programs that draw heavily on system resources capacity becomes a key word. The larger dimm lessens memory holes resulting in better performance all around. On newer systems with newer apps as well as games larger ram is becoming the need there. For single channel mode or on a board that lacks a dual channel mode the larger single dimm would be the best move there.