A while back I found an awesome book that showed the coats-of-arms of most of the towns and villages of Bizkaia. Each town was given a different page, with a drawing of the escudo and some information about the town. I’d always hoped to find something similar for the other provinces, but was never able to. These days, though, if it’s in a book, it’s very likely to be online as well. Thus, it should come as no surprise that there are lists of the municipalities of the various provinces and their heraldry, and maybe the best site for this is Wikipedia.
They have different sections for the coats-of-arms of the towns of Bizkaia, Gipuzkoa, Araba, Nafarroa, and, lumped together with other provinces of the Pyrénées-Atlantiques, Iparralde — the French Basque Country.
I imagine these aren’t complete, but they do give a very nice visual display of the towns and villages of the Basque Country. I think it would be great to also have something about the origins of each individual coat-of-arms, but that is asking a lot.
There are versions of these on the Spanish version of Wikipedia as well, which do give more detail, such as the actual description of the coat-of-arms. For example, see this page for Bizkaia and this one for Nafarroa.