"Export to .inx if you have CS, CS2 or CS3"
You may have text reflow issues.
If you're upgrading it would be better if you upgraded to InDesign CC2014/2015.
Your CS3 files on a MAC will convert to a PC CS6. But you can not go backwards. So, once you open a file up in version 6 you can't open it back up in version 3. At work, I currently use a MAC with a virtual PC on the MAC. I use CS6 (5.5) on the MAC side and then use CS3 on the PC side. It is very frustrating. We are begging for CS6 for our PC side so it will be the same. The reason is because certain systems we use are not available on the other system. I hope that helps. Also if the file is or can be saved as a .inx instead of a .indd you can open it in other versions. If I download InDesign files I always pick the .inx to make sure it opens.
CS3 files will open fine in CS6 but you’re pretty much throwing good money after bad. You can’t buy CS6 without calling Adobe directly so they can warn you that it won’t be supported and has reached end of life. It’s your money of course, but you should be aware of that before making a decision.