When spicing rice, should you add the spices in the water beforehand or after the rice has cooked?

I can only answer from a perspective of the Indonesian kitchen, and my own personal experience, but in general the answer is:

In the water, with the rice

I quite often use saffron, turmeric, cloves, daun salam (The English Wiki entry links to bay leaf, which, completely, utterly, is not the same thing), and lemongrass, and they all go in while cooking the rice.

Possible exceptions would be green leafy herbs, (coriander / cilantro for instance), which you put in the end. Not so much to flavor the rice, but more to "scent" the bowl of rice.

[Edit]

In answer to your edit:

There is no preferred way. The preferred way depends on the herb, as observed by thrig in his/her answer. Going by experience, and the herbs I use myself, the answer is in the water with the rice. Putting a bay leaf in after the fact, is not going to do much for a dish. Putting it in while cooking the dish is. This goes for a lot of herbs: Turmeric, ginger and laos (galangal?) can flavor rice, but not if you put it in the end. On the other hand: Putting cilantro while cooking the rice will just destroy the cilantro, and leave nothing to show for it. I lack the knowledge of what is water-soluble, and what is fat-soluble, but as a general guideline I use my highly personal "is-this-going-to-survive-the-15-to-20-minute-cooking-process-or-not?" guideline, and the even more personal "did-it-work?" guideline.

In addition, and perhaps also supporting thrig's answer, Indonesians are not shy of cooking their rice in santen (again: English wiki does not do justice, creamed coconut is not quite the same), adding a mildy greasy layer to the grains, aiding in flavor absorption, although I have to say it's not a common practice, but more often used for festive occasions.

I think a good rule of thumb is whether or not the spice is dried. For example, dried Rosemary will soften to the texture of the rice if cooked in the water with the rice, but will be crunchy if added after. However, fresh Rosemary can be stirred in after to add flavor.

For a rice cooker of average size, add cumin seeds (1 tea spoon), cloves (4-5), mace (1 piece), cardamom (1-2 pods) and a pinch of salt at the beginning of cooking to get fragrant rice (e.g. for biryani). Add finely chopped mint and coriander leaves after cooking to get the best results. This is a fail-proof recipe to make Indian rice. As you are using rice cooker it will always come out well.

Quantities and timings of adding ingredients DO matter. For example, cumin et al will give out essential oils in the water bath when boiled throughout. Mint and coriander will add nice green colour and fragrance when added just before serving (but will turn black and the fragrance will be lost if added any earlier).

Enjoy :).

Probably depends on whether the spices are water-soluble or fat-soluble; if fat-soluble, and the rice is being cooked without fats, then there's probably little point in adding them to the rice cooker.

"On Food and Cooking" (McGee) has notes on the spices, what chemicals they contain, and more (see: chapter 8). Notably, "oils and fats dissolve more aroma molecules than water during cooking, but also hang on to them during eating, so that their flavor appears more gradually and persists longer." (p.399) Alcohol is also efficient, but has an evaporation problem (and sometimes cultural issues, see e.g. the Eighteenth Amendment to the United States Constitution). Another method besides the already mentioned steaming or frying in oil is to dry roast whole spices (e.g. mustard), which should mellow their effect (and, bonus: no oily pan to wash).