List of common Japanese phrases/sayings/words

Ohayo- Good morning.
Ohayo Gozaimasu- Good morning. This is the more formal equivalent.
Sayonara- Bye
Moshi moshi- The equivalent of hello when one answers the phone.
-san- -san is an honorific, used pretty much universally attached to, typically, the last name. It's very formal.
-chan- -chan is an endearing honorific. It's used to show affection and also between friends. It can also be counted as insulting in the right situation. Typically used for females.
-bo- like -chan, but exclusive to males.
-kun- is used to refer to those of junior status, any males or male friends, and on occasion females that are being addressed by males that they're emotionally attached to or have known for a long time.
-sama- Used to refer to someone higher than yourself.
-senpai- Used to refer to an upperclassman. It can also be used as a word on its own.
kohai- People in the same grade as you.
Sensei- Used in respect typically for someone who has reached a level of mastery in something.
Gomenasai- Sorry.
Gomen- Sorry. This is a much more informal version.
Onegai- Please
Sou ka?- Is that so? or Oh really? It's the informal form of 'Sou desu ka' and typically one would say 'Ah' or 'Oh' before sou.
Kawaii- Cute, adorable.
Baka- Idiot, dummy, etc. Words in that general area. It is, obviously, an insult.

Notes: To clarify about honorifics, honorifics are used in most forms of formal speech. To refer to someone without using an honorific denotes a deep intimacy either between highly close friends or lovers. Typically, until given permission otherwise, one would refer to the other by their last name and proper honorific.
This list is far from complete and I will probably up date it frequently.