On questions, I have the possibility to vote for "close" (as duplicate, say), or to "flag" (as duplicate). Does is it make a difference?
In general, the site is intended to work as a community, so using your votes is the preferred way to push for closing. Flagging is best used for things that really need moderator attention, which is more likely to be true for older questions which might not attract other people's interest than for very recent posts that will (probably) get other close votes.
One point to note is that mods can migrate to anywhere on the StackExchange network. So if you spot a question off-topic for us but on-topic for another site on the network, flagging (in addition to voting) is a good idea.