The size, Thunderbolt, MagSafe, and the other ports on the back of the display.
What justifies the $999 price is the panel. Most 27" displays you'll find run at 1920x1080, use CCFL backlights, and use a TN panel. The 27" Thunderbolt Display runs at 2560x1440, use LED backlighting, and it has an S-IPS panel.
For comparison, look at Dell's U2711, it's priced at ~$825, but has CCFL backlighting. For the $175 more for the Thunderbolt display, you get LED backlighting, and thunderbolt.
What is a TN panel and what exactly is S-IPS? Is there a big difference? Also, what is the difference between CCFL(What's CCFL anyway?) backlight and LED backlights.
What is a TN panel and what exactly is S-IPS? Is there a big difference? Also, what is the difference between CCFL(What's CCFL anyway?) backlight and LED backlights.