I agree to Okada-san's opinion. 魂（たましい） must be an appropriate word though, 立て箸 (to stick chopstick into some food) is one of　Buddhist rite. In Buddhist,'chopstick' represents the bridge between this life and eternity. That is why you shouldn't stick chopstick into some food. In Buddhist (in Japan), the spirits (of the dead) is called '仏(ほとけ）'.　

reference: お箸は、あの世とこの世のかけ橋という意味がありますが、普段（ふだん）は不吉（ふきつ）とされている。
http://www.kodomo-silkroad.net/denpa/food_tool/index.html
'Butsudan' 'family buddhist altar' or 仏壇(ぶつだん） Okada-san mentioned is so-called the dead's(deads') house.
Generally in Japan, chopsticks should not be vertically stuck in the rice, which is done during a Japanese Buddhism-style funeral. During funeral, people put chopsticks in a bowl of rice sticking at the head of the dead as an offering. Generally, many Japanese parents teach their children chopstick manners( including the reasons) as general knowledge.

In Shinto,it is called 御霊（みたま）as Okada-san suggests.
But, if you select it as general term regardless of religion.
魂（たましい) is appropriate word as Okada-san suggests.
立て箸　is Buddhist rite,so I suggested the above.
I hear 御霊（みたま） is the word which has been originally used in Shintoism(神道,http://en.wikipedia.org/wiki/Shinto).

In Shinto, people put steamed rice as an offering, but chopsticks aren't vertically stuck. It's only Buddhist rite. In Japan, it must be ill manner to stick chopstick into some food regardless of whether they are buddhists or not. Some(or many?) Japanese-style tea ceremony(which has been primarily influenced by Zen Buddhism) masters seem to instruct how to use chopsticks as their traditional Japanese customs and manners. I don't know its details, but each manner seems to have reason.


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Note added at 1 day10 hrs (2011-07-19 00:09:09 GMT)
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* 祖先 or 先祖（ancestor）is not appropriate here. the spirits of the dead may include both 祖先の魂 and 'extraneous' ones.