I found a good description of the engine in the Sonic games. It describes roughly how the engine works for people writing their own clones. In my case, I am simply interested in getting a general view of how the many 8-bit and 16-bit game engines worked on their respective consoles. So, this is a big-list style question asking, what other online descriptions of specific game engines have people found?
Most games of that era functioned very uniquely; there was very little engine-like code reuse.
That said, you're fairly likely to find the kind of detailed descriptions of gameplay mechanics you want from games that are very big/popular like Metroid, Final Fantasy 6 or Final Fantasy Tactics -- people have been researching the mechanics of those games extensively and you can find a fair bit of information about them scattered arond. Also games that are popular among tool-assist speed run fans as they tend to have know (and thus, hopefully document) a lot of the interesting quirks of the game code used in the games they run.
(Note that the TASVideos link was being really flaky at the time I wrote this and may not connect reliably.)
There is commented data formats with little code of several 8-bit games, these games are:
I found it interesting that some of them use compression (RLE, dictionary), some of them don't, some use name generators; they had to save space because 8-bit computers had little memory. I believe that by examining these data formats You can derive algorithms yourself. :)
There is more 1 hour long video of making of Google's Pacman clone on Youtube and they used this detailed study of Pacman (Gamasutra link). In video they talk how they used some "good old" techniques like packing multiple textures into one ...