I've always been a big fan of painting models exactly like codex, army book, fluff, and/or real life historical markings and schemes.
I've also been a big fan of, "they're your dolls, painting 'em however you want."
The third choice, however, it to paint them like something else.
I've thought long and hard about painting a Cadian Imperial Guard army up like GI Joe and Cobra. The Cobra half would be a blob squad with a couple of characters like Destro, Cobra Commander, and the Baroness. The Joe half would be veteran squads with heavily converted models to make up all of the "good guys." Duke, Flint, Gung Ho, Snake Eyes, and Beachhead were my favorites. Tunnel Rat too.
I've seen a couple of others before, but I really like the look of this guy's Cobra army:
Cobra Themed GI Joe - Imperial Guard Army
Other cool models I've seen have been the Gundam Tau:
A whole bunch of Avengers: