I'm assuming you want to save things you downloaded... the instructions below should save everything but you may have to set it back up once the game reinstalls.
Go into your game and drag your course folder(the one with all the courses if you made a 2nd one for quicker startups),the polyAni folder(your player ani's and clubs) to your desktop. If you have sound files you want to save do the same to LINKSND,and WAVS,
Then go to my documents and do the same to the links 2003 file. After reinstalling replace those folders into the game overwriting the ones the game created during the reinstall.
go here for all the patches
viewtopic.php?f=2&t=8533