About the color emphasis thing... I uploaded a copy of a doc about it here:
http://www.geocities.com/disch_/Chris_Covell_Colour_Doc.txt

I couldn't find this doc on nesdev anywhere... but maybe I just overlooked it or something.

About the sprite positions (like the SMB issue)... the only thing I can think of is you're not handling the sprite coords correctly. Either that or it's a CPU issue (but that would probably cause other problems in games and not just graphical glitches).

As for games which use 8x16 sprites... Zelda, Zelda2 and SMB3 are the first to come to mind.