3.8 GPA, but 3 Fs and 1 D on transcript
In my (rather extensive) experience with graduate admissions, admissions committees understand that people have semesters in which life interferes with school. If you've retaken the classes and received high marks in them, this very clearly signals that something was interfering with your performance during those two semesters and that the bad grades have nothing to do with your underlying ability. Those grades won't go unnoticed -- but nor will they hurt you the way they would had you not repeated and aced those courses. 

It would help further if you have a trusted mentor who could mention and--to the degree that you comfortable, explain--this issue in his or her letter of recommendation. 

Don't count on cruising through the application process, but also don't lower your ambitions based on these grades.