I do this all the time and I always book the C-B flight connecting to the next A-C flight. I am rarely time constrained and spending a day in a hotel is not a big issue for me (I work remotely anyways). Yes, this means the cost of the hotel needs to be factored in. However, as mentioned in the original post, you might be doing this for other reasons than finding the cheapest possible flight and I often do. Although my examples are also for cost reasons but nowhere near the cheapest economy tickets.
I was flying from Vancouver to Wellington so I took Westjet to Honolulu, slept there, then used Jetstar to Wellington via Sydney. As I really hate economy seats for longer flights, on Westjet, I had an extra legroom seat (doable for six hours) and on Jetstar to Sydney I was flying business class (only thing I would do for such a long flight). Buying a single business class ticket from Vancouver to Wellington was about three times as much as what I spent on this. Not to mention that flying from the west coast to Australia/New Zealand is 15-ish hours and I can't imagine doing such a long flight: I'm OK w/ 10 and get antsy on 12 hours even in business. 6, sleep, 10.5 is much better for me.
Another example. Delta had a crazy business seat sale for Seattle-Frankfurt and my destination was Budapest so I took the bus from Vancouver to SeaTac then slept there, took Delta to Frankfurt, slept there (see a pattern?) and then took Lufthansa to Budapest the next day.