There are four base configurations, two 21.5-inch options and two 27-inch options. Luckily the differences are pretty straightforward, which should make your choice easier. Let's start with the two 21.5-inch models.
iMac 21-inch 2.7GHz vs. iMac 21-inch 2.9GHz
1) 2.7GHz Quad-core Intel Core i5 vs. 2.9GHz Quad-core Intel Core i5
2) NVIDIA GeForce GT 640M w/512MB vs. NVIDIA GeForce GT 650M w/512MB
3) $1299 MSRP vs. $1499 MSRP
For an additional $200, you receive an incrementally faster processor and a slight graphics card upgrade.
If you look at the differences between the high-end iMac 21.5-inch and the low-end iMac 27-inch you will notice a $300 price differential for the jump from 21.5-inch to 27-inch. The hard drive is slightly faster in the 27-inch and the graphics card is incrementally better. The rest of the specs are identical.
If you compare the two 27-inch options, again you will see just a few differences.
iMac 27-inch 2.9GHz vs. iMac 27-inch 3.2GHz
1) 2.9GHz Quad-core Intel Core i5 vs. 3.2GHz Quad-core Intel Core i5
2) NVIDIA GeForce GTX 660M w/512MB vs. NVIDIA GeForce GT 675MX w/1GB
3) $1799 MSRP vs. $1999 MSRP
Notice the $200 gap between models for a processor boost and graphics card upgrade. I would probably choose the low-end 21.5-inch or low-end 27-inch because the upgrades to the higher-end models do not seem worth the cost. Instead, you could buy a separate 16GB RAM upgrade for $75-$100 to get a real performance boost that is also cost-effective via Apple Sliced Memory
. Please note that the RAM in the 21.5-inch model is not user-upgradeable.