Don't do it! There'll be many users of your application that will happily slap you back into stone age. I'd say about 100 rows should be the limit, that a user can handle.
Provide filters that reduce the number of row to a tolerable level.
I hope by now you realize you won't get people to design the stuff for you. That's your job as a programmer and also to perform the research required to do whatever solution you come up with.
It seems to me that you want to mimic pagination that you see often in web applications. You want to give the user the opportunity to navigate the huge pile of results you may have, but you display only a limited set of the total result (say - 100 items per "page") as to not bog down the user interface and drive up the resource usage.
Now lets say that you agree with me and that is what you want: what are you going to do? Are you going to ask how to do that, or are you going to google "java swing jtable pagination" ? I hope the latter.