Phoneme
A phoneme is the smallest phone (unit of sound) that is distinct from other phones.
What constitutes a phoneme is very very dependant upon your language and upbringing. For example, consider P with a) no aspiration, b) a little aspiration and c) a lot of aspiration. In English these three allophones are all the same phoneme. There are languages (which escape me at the moment) for which these are three distinct phonemes.
Similarly, rumor has it (I don't know if this is actually true) that L and R, while distinct phonemes in English are the same phoneme in Japanese.----
I would say a phoneme in a particular language is the smallest unit of sound which distinguishes pair of words in that language. For example in English, we must find a pairs, like "bit" and "but" and "bit" and "bat" to decide that /i/ is a phoneme. And yes, in Japanese, "r" and "l" sounds are one phoneme, pronounced somewhat like an "r" (flap).