1.) Which is the best choice for the blank?
2.) What is the best choice that you have made?
Which are the subjects in the above respectively?
Yes, "Which" and "What" can be considered to be the grammatical subjects.
It is also reasonable to consider that the noun phrases headed by the word "choice" are the grammatical subjects.
Usually, subject-auxiliary inversion can help in pinpointing the grammatical subject of a sentence.
Creating similar example sentences by expanding the, er, verb phrase into using multiple verbs, which includes an auxiliary, can often be helpful. In your case, by doing that, we can get:
1.b) Which will be the best choice for the blank?
2.b) What will be the best choice that you have made?
These two new versions (#1b and #2b) have meanings that are somewhat similar to those in the original two examples. Notice that there is nothing in between the auxiliary "will" and the verb "be", and so, that means that there hasn't been any subject-auxiliary inversion, and that means that the subjects are "Which" and "What".
Since the subjects in #1b and #2b are "Which" and "What", that means that the subjects in the two original examples (#1 and #2) in the OP's post can also be "Which" and "What".
As a reaffirming sort of test: For these four examples, these could be the associated declarative clause versions,
1.c) Answer D is the best choice for the blank.
2.c) Staying single is the best choice that you have made.
1.d) Answer D will be the best choice for the blank.
2.d) Staying single will be the best choice that you have made.
All four of the declarative versions sound reasonable.
Though, do note that the two original examples could be interpreted as having gone through subject-auxiliary inversion already, and so, that the subjects could be the noun phrases headed by the word "choice":
The in situ versions of these interrogative clauses -- where the subject is now located in the front -- could be:
Here's a related post (which is even longer) on this topic: