Let's see, going back to Jessica Blake being Marie's grown daughter (Marie knew she gave birth, but did it secretly and placed the child in a convent).
Stefano being father to Renee, Lexie, Chad and Andre were all surprises (he knew he was father of Megan, Benjy and EJ; and Tony, sort of)
Cassie and Rex being the children of Roman and Kate, carried by Marlena.
Lucas being a surprise son to Bill Horton.
Billie and Austin (although Kate knew she gave birth to them, she thought they were dead)
Melanie being Daniel and Carly's surprise child.
Daniel being Maggie's eggbaby.
Summer being Maggie's daughter.
Brandon and Lani being Abe's children.
Paul being John's son.
Isabella and Bo being Victor's children.
Chelsea being Bo and Billie's daughter.
Eve being Shane and Gabrielle's daughter.
Paige being a secret Hernandez child.
Roman was surprised by Carrie, as he thought a pregnant Anna died in the boating accident.
Eli Grant is the son of David Banning and Valerie Grant.
Chloe being Nancy's secret daughter, later finding out she was Craig's daughter, too.
Nicky Alamain was thought to have died at birth, was later discovered to be Carly and Lawrence's son (but Vivian knew).
Donna Craig was Don Craig's surprise teenage daughter.
We can kind of count Quinn Hudson being Vivian Alamain's secret son, but it was only a secret to the viewers, not her.
And now, Steve has a surprise son, Tripp.
I'm sure there are more, but these are the ones I could think of at the moment.