Can I say a brachah with just boxers on, or do I need a "double covering" For example, when I wake up and want to wash netilat yadayim?
The Shulchan Aruch rules (OC 74:6):
The operating principle here is twofold:
Thus, one could not wear a t-shirt and put a bag on his head, as this would violate the first principle. Additionally, one could not wear just a toga as this would violate the second principle.
Assuming then that your boxers are snug with your waist (usually due to elastic) such that your heart cannot see downwards, then you may recite the Shema and all other blessings (with the exception of Shmoneh Esrei for which you must look like you are approaching a king, ie with clothing on.)