Step 1: Examine the features of Archaea and Bacteria.
Archaea and Bacteria are both prokaryotic organisms, but they differ in several fundamental ways.
Step 2: Analyze the options.
Gram-staining (A) is a method to differentiate bacteria based on the structure of their cell walls, but it does not differentiate between Archaea and Bacteria. Both Archaea and Bacteria can be Gram-positive or Gram-negative.
Peptidoglycan in the cell wall (B) is a feature of Bacteria. Archaea, on the other hand, lack peptidoglycan in their cell walls. Archaea have a variety of different compounds in their cell walls, such as pseudopeptidoglycan.
Presence of N-acetylglucosamine (C) is found in both Archaea and Bacteria, so it is not a distinguishing feature.
16S rRNA sequences (D) are used to distinguish between Archaea and Bacteria. The 16S rRNA gene is highly conserved in both groups, but there are distinct differences in the sequences that allow for their differentiation.
Step 3: Conclusion.
The two primary features that distinguish Archaea from Bacteria are the absence of peptidoglycan in the cell wall of Archaea and differences in their 16S rRNA sequences.
Thus, the correct answer is \( \boxed{(B), (D)} \).