Biggest difference will likely come from SSD. Next, consider a RAM upgrade (cheapest upgrade). Next, look at CPU/GPU/motherboard upgrades (more expensive, and need to check compatibility with other components).
Not sure what you use it for, but for $999 you can get a new MBP basic level (or maybe it's a MBAir?). If you're a light use, upgrading SSD and RAM will show a big boost for 2-300 $$.