I usually play with the Dutch. The English are OK too.
Founding Fathers
The relative importance of the founding fathers depends on your playing style. Given the way I play here's what I recommend.
William Brewster should be your top priority. Indentured servants and criminals are a real pain. If you get some at the beginning turn them into soldiers or pioneers.
One of my next choices is Pocahontas. The Indians tend to get annoying after a while and Pocahontas appeases them considerably. Also, you can 'steal' all the Indian land around your colonies one turn before she joins the continental congress without suffering the consequences (saves you from having to get Peter Minuit).
Get Thomas Jefferson, Thomas Paine, and Simon Bolivar as soon as you can.
You should also consider getting Benjamin Franklin pretty early on. It's almost inevitable that other powers will come bother you (put wagon trains on your road squares to keep the enemy dragoons from blocking them up). A war is expensive and wasteful, particularly against the AI that seems to have an almost limitless source of dragoons.
Hernando de Soto can be important since he will significantly increase your chances of finding fountains of youth.
Other founding fathers that are useful but not necessary are Ferdinand Magellan, John Paul Jones, Peter Stuyvesant and William Penn.
Colonies
I like to build few colonies and build those up quickly to take advantage of economies of scale. I recommend only three main colonies (there's less micro-management and you'll be ready for revolution sooner). Ideally they will be no further than three squares apart so that you can move units in one turn by road. One of the colonies should be next to a silver mine (it's also OK to build a small inland colony with the sole purpose of mining silver). It's best to build only one or two coastal colonies and the other one(s) inland. This greatly facilitates defense during the revolution, as you will pretty much know where the REF will land. Each colony should have at least two squares of forest, and at least one square of hill or mountain (two are preferable). The cities should not be very far away from where you start to reduce the time it takes to get to and from the Old World. You'll need a lucky start for this to work best.
Colonists
Having a constant supply of colonists is one of the main challenges of the game. Here are some ways to get them:
Recruit or train them in the Old World. This is expensive but often necessary.
Send out missionaries to convert Indians. The Indians aren't as good as experts though so I don't really like this method.
Produce lots of crosses. This is difficult to do at the beginning. You should build churches and cathedrals. Firebrand preachers really help. So does William Penn.
Build up food. If you accumulate 200 food you get a free colonist. However, I tend to prefer using the food for horses.
Capture colonists from computer players. This is especially useful at the beginning.
Fountains of youth. These give you 8 colonists. Make sure you have William Brewster and Hernando de Soto before you uncover the lost city rumours. Fountains of youth are pretty rare but I don't think there's a limit to how many you can find. In one game, I found 3. Send out scouts everywhere.
There are rare instances--particularly at the beginning of the game when rebel sentiment is still low--when you have more colonists than your colonies can absorb. In that case turn some of them into pioneers (don't forget to buy lots of tools). Leave two squares of forest (conifer forest is preferable) around your colonies and plough all the remaining land. Don't forget to plough the colony square (twice if you built in a forest). Build roads on forest and hill/mountain squares. Also build roads to connect your colonies. Make sure that the connecting roads do not run along the coast since otherwise they will get blocked during the war of independence.
Rebel Sentiment
The biggest problem in Viceroy is that you need a strong rebel sentiment before you can really grow your cities. The first person to put in a city is a statesman. Next you need a farmer and a lumberjack (when your lumber supply is full, turn the lumberjack into a carpenter). As rebel sentiment increases you will be able to slowly add more people without getting production penalties. Always put as many statesmen into a colony as you can. With the money you get from selling the silver you should buy an expert silver miner and an expert statesman as soon as possible. Put the elder statesman in your most promising colony. It's impossible to grow a colony quickly without an elder statesman. In fact if you can afford one for another colony, it's an excellent investment. The +1 production bonus at 50% rebel sentiment and the +2 production bonus at 100% really help a lot. Printing presses and Newspapers are key.
Things to Build
First thing to build in a colony is a lumber-mill as this will double your production speed (the colony must be at least size 3 to build one). Next in order of importance is a printing press and a newspaper. These require tools that you should buy in the Old World. It's a good idea to buy lots of tools at the beginning since they are hard to produce in small colonies. Also they are cheapest early in the game. In your biggest city (the one with the elder statesman) you should then start to build a schoolhouse, college and university. To build larger structures like a university you will need a warehouse first.
You will need churches and cathedrals to attract more colonists. Churches and Cathedrals are also useful places to put free colonists to be trained.
Before you declare independence make sure you have Fortresses in your coastal colonies.
Last thing to build is an armory and then simply crank out artillery units.
Training colonists
This is what the game is really about. If you don't already have an expert farmer and an expert fisherman, buy one of each. Then put them in your schools and start training colonists. Every time a colonist learns a skill send him out to where he is needed and send a free colonist back to be trained. This way you'll rapidly have experts providing food. Then start training lumberjacks and carpenters. A little later ore miners and blacksmiths will become very important. As soon as you have a university start training elder statesmen. Once a statesman is trained put him in the university too until you have 3 statesmen teaching. Count how many experts you'll need for all your cities. For instance, you'll need 9 elder statesmen, around 6 or more expert lumberjacks, 8-9 master carpenters etc. The idea is to have only experts in all your cities. Firebrand preachers can be useful but train them only after you have all the elder statesmen you need and you have built cathedrals in your colonies.
Preparing for War
Once you have all the experts you need, start training veteran soldiers. Build as many artillery units as you can. Also, start producing muskets. Be very careful not to produce too many muskets or else you won't have enough tools to finish the artillery units. Build a stable in colonies that have excess food. Put in at least 50 horses and let them breed. Store excess muskets and horses in wagon trains once your warehouses fill up.
Declaring Independence
You have to be quick in Viceroy because another power will usually declare independence in 1660-1680 and you want to be first! You should have AT LEAST 25 artillery units and about the same number of soldiers (dragoons are of course preferable). You should also have a stockpile of muskets. Each colony should be producing 152 liberty bells per turn. Still, you'll have to hold out quite a while before you get help from another nation. You'll definitely need that help to the defeat the 110+ units of the REF.
The REF always lands near your weakest coastal colony. Move reinforcements into the colony that's being attacked. Make sure you have a couple dragoons on hand to attack any units that may block your roads. Just stay in your fortresses and defend, your odds are much better. You should win the war pretty quickly (about 20 turns).
Getting a High Score
Just like in Civ2, getting a high score is more of an exercise in patience than in skill (there are many tedious ways to 'exploit' the scoring system). I think that an early revolution is a more worthy (and fun) goal.
See my saved game in the High Scores section for an example of my strategy.