[chryuop]

It is kinda hard to ask for the most common suffix, coz they all have different meanings so you will find them in different occasions. For example they put in the list mashita, but the ta itself is a suffix (past tense particle).
Then you have to specify what you call suffixes. In english a suffix is just made of few letters which show a certain class a noun belongs to which don't have a real meaning taken alone (er, ish...and so on) and in very few cases can be a word (like, hood...).
Now what you might think a suffix it might not be. It might be a simple particle like ta, te rareru and so on... It might be another verb as in 私はｵﾍﾟﾗに行きつけている (watashi ha opera ni ikitshuketeiru=I often go to the opera) where the verb つける in this case goes after a verb and means being used to. It might be an adjective like in ｲﾀﾘｱへ帰りたい (itaria e kaeritai tai=I want to go back to Italy) where tai gives the verb a value of desire, wanting. But if you want you can find things like nouns (as in こと koto) or preposition (for example に ni used with combinations with verbs come/go).

In my opinion the range is too big to say the most used. The only thing is study and with time you will encounter them all. Thanks to MMM I just found out another suffix which wasn't even in my dictionary...so patience Luke Skywalker, take one step at the time.

Just my 2 cents....