Sounds like you may want to look into using tables in Excel and capitalizing on their features like filtering and equation autofill. You may also be interested in using a PivotTable to do something very similar to what you're describing.
If you really want to go about this the programmatic way, I think the solution Matt gives answers your question about how to do this using CountIf. There's a big detriment to using CountIf though, in that it's not very computationally efficient. I don't think the code Matt posted will really be practical for processing the 100K rows mentioned in the OP (Application.ScreenUpdating = false would help some). Here's an alternative method that's a lot more efficient, but less intuitive, so you'll have to decide what suites your needs and what you feel conformable with.
Sub CountOccurances()
'Define Input and Output Ranges
'The best way to do this may very from case to case,
'So it should be addressed seperately
'Right now we'll assume current sheet rows 1-100K as OP specifies
Dim RInput, ROutput As Range
Set RInput = Range("D1:D100000")
Set ROutput = Range("E1:E100000")
'Define array for housing and processing range values
Dim A() As Variant
ReDim A(1 To RInput.Rows.Count, 0)
'Use Value2 as quicker more accurate value
A = RInput.Value2
'Create dictionary object
Set d = CreateObject("Scripting.Dictionary")
'Loop through array, adding new values and counting values as you go
For i = 1 To UBound(A)
If d.Exists(A(i, 1)) Then
d(A(i, 1)) = d(A(i, 1)) + 1
Else
d.Add A(i, 1), 1
End If
Next
'Overwrite original array values with count of that value
For i = 1 To UBound(A)
A(i, 1) = d(A(i, 1))
Next
'Write resulting array to output range
ROutput = A
End Sub
You can also modify this to include the removal of replicates you mentioned.
Sub CountOccurances_PrintOnce()
'Define Input and Output Ranges
'The best way to do this may very from case to case,
'So it should be addressed seperately
'Right now we'll assume current sheet rows 1-100K as OP specifies
Dim RInput, ROutput As Range
Set RInput = Range("D1:D100000")
Set ROutput = Range("F1:F9")
'Define array for housing and processing range values
Dim A() As Variant
ReDim A(1 To RInput.Rows.Count, 0)
'Use Value2 as quicker more accurate value
A = RInput.Value2
'Create dictionary object
Set d = CreateObject("Scripting.Dictionary")
'Loop through array, adding new values and counting values as you go
For i = 1 To UBound(A)
If d.Exists(A(i, 1)) Then
d(A(i, 1)) = d(A(i, 1)) + 1
Else
d.Add A(i, 1), 1
End If
Next
'Print results to VBA's immediate window
Dim sum As Double
For Each K In d.Keys
Debug.Print K & ": " & d(K)
sum = sum + d(K)
Next
Debug.Print "Total: " & sum
End Sub