The main thing to understand with generic types, is that they aren't covariant.
So whilst you can do this:
final String string = "string";
final Object object = string;
The following will not compile:
final List<String> strings = ...
final List<Object> objects = strings;
This is to avoid the situations where you circumvent the generic types:
final List<String> strings = ...
final List<Object> objects = strings;
objects.add(1);
final String string = strings.get(0); <-- oops
So, going through your examples one by one
1
Your generic method takes a List<T>, you pass in a List<?>; which is (essentially) a List<Object>. T can be assigned to the Object type and the compiler is happy.
2
Your generic method is the same, you pass in a List<List<?>>. T can be assigned to the List<?> type and the compiler is again happy.
3
This is basically the same as 2 with another level of nesting. T is still the List<?> type.
4
Here is where it goes a little pear shaped, and where my point from above comes in.
Your generic method takes a List<List<T>>. You pass in a List<List<?>>. Now, as generic types are not covariant, List<?> cannot be assigned to a List<T>.
The actual compiler error (Java 8) is:
required: java.util.List<java.util.List<T>>   found:
  java.util.List<java.util.List<?>>   reason: cannot infer
  type-variable(s) T
      (argument mismatch; java.util.List<java.util.List<?>> cannot be converted to java.util.List<java.util.List<T>>)
Basically the compiler is telling you that it cannot find a T to assign because of having to infer the type of the List<T> nested in the outer list.
Lets look at this in a little more detail:
List<?> is a List of some unknown type - it could be a List<Integer> or a List<String>; we can get from it as Object, but we cannot add. Because otherwise we run into the covariance issue I mentioned.
List<List<?>> is a List of List of some unknown type - it could be a List<List<Integer>> or a List<List<String>>. In case 1 it was possible to assign T to Object and just not allow add operations on wildcard list. In case 4 this cannot be done - primarily because there is not a generics construct to prevent add to the outer List.
If the compiler were to assign T to Object in the second case then something like the following would be possible:
final List<List<Integer>> list = ...
final List<List<?>> wildcard = list;
wildcard.add(Arrays.asList("oops"));
So, due to covariance, it is not possible to assign a List<List<Integer>> to any other generic List safely.
>` means a `List` whose elements have the type `List>`, whereas `List>` means a `List` of some unknown type.
– Paul Boddington Apr 09 '15 at 06:45