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The two I would say you must get: peppercorns (black, green, white, or mixed) and cinnamon. Yes, these are very common spices that are widely available around the world, but the pepper and cinnamon that I got in Kerala are the best I've ever had. (Bonus: You can buy cinnamon bark in a fresher state; flat bark pieces rather than the curled, stick-like cinnamon that is the final product of a full drying. The flat bark works great for infusing cinnamon flavor - throw pieces into hot apple cider, rice when you're cooking it, any curries. It's delicious.)
The Wikipedia page for cuisine of Kerala lists cinnamon, cardamom, ginger, green and red peppers, cloves, garlic, cumin seeds, coriander, turmeric as the most common spices. (I don't know why green and red peppers are listed there; I think I'm not sure whether they mean bell peppers or chili peppers.)
This Kerala tourism site has a similar list, but it provides more information about the varieties available and which reasons they're grown in.
Cardamom, clove, vanilla, tamarind, and turmeric are all popular, too. It looks like Indian saffron is usually grown in Kashmir, so you might be better off buying that in Delhi. Many Indian spices are grown widely throughout India, so you could theoretically purchase all of your spices in Delhi; I lived there for a short while and every spice that I found in markets when I visited Kerala were also present in Delhi spice markets. Merchants in Delhi often market their spices as being from Kerala. However, I would definitely buy pepper and cinnamon in Kerala still. Try eating fresh peppercorns (not cured/dried) if you get a chance, too!
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You mention that will be travelling for a long time. This makes the possibility that the spices you're carrying will get damaged in transit (moisture leaking into containers). None of the spices mentioned in Laura's answer are particularly that expensive so if you're ultimately flying out of Delhi, you might just want to buy them from open-air vegetable markets in Delhi itself which in itself is a unique experience. (For lower prices, shop in areas of Delhi with higher concentrations of South Indian population, such as RK Puram.) The exception is saffron - while saffron is used in many different Indian cuisines, it's mostly grown in Jammu & Kashmir, and it's definitely cheaper to buy saffron there if you're going.
And while they aren't spices, I would also recommend buying tea or coffee if you're into that. Normal tea is better in Darjeeling (east India) but in Southern India, you can get really good flavoured teas such as cardamom tea for cheap.