For the 30s and 40s, my favorite is the venerable flathead because it can be built so many ways but always looks cool!
For the 50's and 60's I'd have to say the 409 and the HEMI - with either one of them, you know what it is just by looking at the valve covers.
For the 70s and 80s I'd have to give the nod to the Boss 351 Cleveland engine. Again for the really cool valve covers.
For the 90s, I really like the Lotus designed, Mercury Marine built (LT5) ZR-1 because it is so distinctive looking. Sure, it's not fully domestic, but they came in Vettes.
Then there's a whole list of exotic engines (Ferrari, Lamborghini, Lotus...).
So, what's your favorite engine and why?