Well, I've played the game through six times, each time running with a single god.
As far as the gods themselves go, I like Persephone best. Yes, she's self-righteous, but she's the only god in the pantheon who isn't particularly silly. It's a pity she doesn't make it through the game...
As far as divine groupings go, I'd have to go with Persephone again. Liberal use of lifeshield and healing spells makes defeating any enemy a breeze, even if she's kind of lacking in the destruction department. Unlike the other deities, Persephone does not have any units that I would never want to use. Dragons are amazing when it comes to destroying manaliths, and while it is true that they're not good at attacking in large groups (large melee unit = size issues), they're quite powerful.
However, if I had to make a unique combination...
lvl 1: I'll start with James. The Trogg's magic-resistance is very useful. In fact, all of James' low-level units stay useful even at higher levels, provided that you have enough of them. Yes, the flying rock spell has a tendency to hit my flyers, but I can live with that.
lvl 2:Persephone for level 2, I think. Ethereal form is nice, and the scarabs are helpful when you don't want to spend a lot of time healing your units.
lvl 3:Persephone again. Regenerating troll units with a good melee attack and a solid halting spell.
lvl 4: The fourth level is tricky. Persephone's rainbow spell is excellent, and the gnomes are nice. On the other hand, Charnel's animate dead spell is arguably the single best "healing" spell in the game, good enough that I'm wiling to overlook how troublesome the necrofiends are. Probably the ultimate winner is Stratos, because chain lighting and storm giants make for an excellent combination.
lvl 5: The fifth level is even tricker, because at this point almost no god has anything really good. The award then passes to Charnel, because of the accuracy of demonic rift and the inarguable utility of the Deadeyes.
lvl 6: Sixth level can go one of two ways. If I know I'm going to stop development at this level, I choose Persephone. The mutants' attack range is excellent. A lot of people have brought up the Boulderdash at this junction: I don't care for the boulderdash because it always hits my flyers. However, if I'm going forward another level, I'll go with the boulderdash anyway, because it makes for a great combo with what comes next.
lvl 7: This is a tricky level (everyone starts pulling out their biggest guns here), but in light of the units I've already got, the award passes to Pyro. The warmonger is destruction incarnate. A large, mixed group of warmongers and boulderdashes (or bombards) can basically ensure that the enemy never gets close enough to deal damage. Rain of Fire isn't bad either. Persephone is the runner-up, because Ents with lifeshield on are truly impressive as meleers.
lvl 8: There's no units at this level, so the gods get judged on the basis of their spells alone. Charm is good, but Meanstalks is not. Bovine intervention is too slow, while Bore is only useful if your timing is very good and you're not playing against a human enemy; another player is smart enough to move out of the way, and even if it works, you can't get the souls of the creatures you kill with Bore. Cloudkill is an excellent spell IF it gets combined with a set of Stratos units like Yetis, while tornado makes for an excellent wall. Intestinal Vaporization is good, while Death is as likely to attack you as he is your enemies.
All things considered, the award goes to Pyro. The volcano spell is great for casting at any large group of enemies, and especially next to enemy manaliths. Rage can defuse an enemy army in moments, making them easy prey for your forces.
lvl 9: Ah, the ultimate units. All powerful, all excellent, all destructive.
The Dragon has excellent damage and defense capabilities. If you have three or four of them, they can also keep resurrecting eachother. But if you have animate dead, there's no point to their special ability, and they aren't really effective in groups of more than six.
The Hellmouth doesn't do a lot of damage, and it isn't very tough. Only its vampiric abilities save it from being dismissed outright.
The Rhinok is the only landbound ultimate unit, and it's very slow. Then again, they are also EXTREMELY tough and their halo of rocks ability basically ensures that a group of Rhinoks will always win against any other opponents, including flyers. James gets my first choice for this reason.
Silverbacks are useful mainly for their freezing ability. They don't seem to do a lot of damage and they are probably the most fragile of the lvl 9 unit types.
Pyro's Phoenix gets my second choice, because they are tough and their death-rays deal a fair amount of damage. They can't match the Rhinoks for sheer power, but they make up for that with mobility.