#46 Wormadam - Catch a Burmy (must be female to get Wormadam) in a Honey Tree and evolve it by level up.
#53 Combee - Catch in a Honey Tree.
#65 Ambipom - Catch an Aipom in a Honey Tree and level up with a Double Hit. Whatever that is...
#80 Barboach - Fish with the Good Rod.
#135 Lumineon - Fish with the Good Rod for a Finneon and evolve it by level up.
#146 Uxie - Found in the cavern at Lake Acuity.
#147 Mesprit - Found in the cavern at Lake Verity, but it runs off and you need to track it down with the marking map to catch it in the wild. It's easier to track it down than you think, so don't use your Masterball on it.
#148 Azelf - Found in the cavern at Lake Valor.