Francis I established the right of the French crown to award bishoprics and other church benefices to its own candidates, which went a long away towards preventing the formation of a Gallican church along the lines of the Church of England. This also means the average church position was a political job, and the majority of bishops hardly ever visited their own cathedrals. The average village priest was usually a sub-contractor, earning very low wages to care for the flock of the official holder of the benefice (who collected its revenue). Every prominent family made a point of putting a son into a lucrative church position, where they often wielded a great deal of political influence on behalf of the head of house: examples include the Duc de Guise and his brother the Cardinal de Lorraine, Admiral Coligny and his brother the Cardinal de Chatillon, etc. A number of such positions were essentially "hereditary" to certain families.
In spite of the religious wars, the Catholic church remains powerful and will continue to be so. In the South, the Huguenot churches established what resembled a kind of independent religious republic ruled by councils of elders. These functioned rather well when there was essentially no government, but they could not approach the power and wealth of the established church. There was a strong "congregationalist" streak among many of the Protestant churches (i.e. independent churches ruled by an assembly of the congregation). As pastors trained in Geneva began to serve these congregations, this independence eventually gave way to the "presbyterian" model promoted by Calvin (with churches ruled by pastors and elders in a hierarchy intended to enforce doctrinal purity).
The second estate is the nobility, who are also exempt from taxes on the theory that they serve the state by offering the king their lives in military service. The old feudal role of the knightly class has been breaking down for some time, but it is taking them a long time to realize it. Royal service has long been their prerogative, but they have been replaced by bourgeois magistrates who are cheaper, harder working, and more loyal to the crown. An increasingly money-driven economy makes living off your own land a much more difficult prospect than it used to be. The nobility depend on war to make money -- ransoms, loot, and royal appointments. A major French defeat (like Pavia under Francis I) can bankrupt families. And if there is no major war to undertake against foreigners, it is only a matter of time before the French nobility start making war on each other. While many military leaders in the religious wars were certainly motivated by conscience (usually in the person of their wives and mothers), for many it was just an opportunity to make a living and they changed sides as necessity dictated.
It was not acceptable for a nobleman to do much of anything except serve in the military, in the royal service, or in the church. Engaging in commerce or mercantile activity, let alone manual labor, could result in derogation -- the loss of all noble privileges for him and his descendants. Worst of all, he lost his exemption to the "taille" -- the tax on the laboring class. Jehan would worry about this a whole lot more if he weren't so broken and jaded, but he’s still somewhat more ashamed of how he makes his living than he is of murdering a man for his boots. Among other things, a nobleman of France had the right to wear a sword any and everywhere, including in the presence of the king. There is an engraving of a gentleman wearing his sword to play tennis. Note that dueling was not made illegal until 1609, when a protracted peace was starting to take its toll on the nobility.
The idea of "clientage" is key to understanding the nobility of this age. This overlaps the traditional feudal concept of vassalage, which is less important now. A noble family cultivated a following of noble clients, giving them appointments, benefices, pensions, etc. in return for loyalty and service. (e.g. When you got someone a job in the tax department, you expected them to do you little favors in return.) Clients of the great would in turn have their own clientage, and so on. When the head of a great house made a move (had a religious conversion, declared for or against this or that policy or person or ruler), he took a whole pyramid of clients with him and could shift the balance of power in France. The right and ability to dispose of patronage is what kept the machinery of the great houses running. The crown used the same technique to manage the great houses themselves: paying them pensions to keep them quiet and giving them choice royal appointments. Paying pensions to the nobility eventually consumed about a third of the royal budget.
The traditional nobility is the noblesse d'epee (nobility of the sword), but this century has seen the rise of a new nobility: the noblesse de la robe (nobility of the gown). This the magisterial class that administers royal justice and the civil government. In France, the Parlements (there is one in Paris and several provincial ones) are more like judicial courts than legislative bodies (as in England). Most of the men of the gown rose from the wealthy merchant ranks. They studied law and made enough money to buy a government office. During this century, the venality (selling) of public office became a plague. The crown needed money, and one way of raising it was to sell government jobs to the nouveau-riche. Most of these jobs came with grants of nobility and excellent opportunities for graft. It was considered a better deal to invest in a venal office (which you could pass onto your heirs) than to risk your money in some kind of commercial venture like the East India Company. Financial positions in the government had traditionally been venal, but it was Francis I that made judicial positions venal. There is a vast amount of resentment between the men of the sword and the lawyers who are buying up their estates as the warrior class goes bankrupt.
The third estate, those who worked, covered everyone from the rich merchant who loaned money to the king to the poor share-cropping peasant who owned little more than his shirt. These are the people who paid the bulk of the taxes. Traditionally, it had been in the best interests of the seigneurs to keep taxes low, as it impacted what they themselves were able to collect from their own peasants. During this century, however, as the pattern of landholding changed from tenant peasants who held lifetime rights to sharecroppers with short-term contracts, the seigneurial solicitude for peasant welfare decreased. 1594 saw a significant peasant uprising (the Croquants), as the depredations of war, bad harvests, inflation, and seigneurial exactions all came to a head. Note that during the war years the peasants often paid their "taxes" several times over, but the royal treasury rarely saw any of it.
Unlike in England, the Netherlands, or the Italian city-states, the pursuit of wealth was not respected. Wealthy bourgeois remained members of the third estate, and the wealthier they were, the more the crown suspiciously eyed their money. During fiscal crisis, it wasn't unusual for the leading citizens of Paris to be "encouraged" to make "loans" to the crown. During this time of upheaval, as noble houses became extinct or fell into debt to the merchant class, the bourgeois bought up noble estates. The French have always had an almost mystical reverence for the land. The new owners of a noble estate could become ennobled themselves if they and their descendants lived on the estate for 40 years and provided the required military service. Many of these new arrivals brought the bourgeois habits of careful business management to these estates, making them more profitable than they had been under their previous owners. Of course, they also favored the more lucrative sharecropping arrangements for working the land, which made the rural peasantry even poorer and more disenfranchised than they had been.
The peasants have suffered terribly in the later half of this century. The early part of this century was quite prosperous and saw a big increase in the population. However, this lead to land being subdivided into economically unviable plots. Although inheritance laws varied by region, farmers divided their land fairly equally among their sons in many parts of France. The religious wars bred a generation of anarchic lawlessness, pillage, extortion, and inflation that collapsed the rural economy. And on top of it all, the weather has been bad. Many peasants have lost their rights of tenancy to debt and have become marginal sharecroppers, while a few of the more prosperous peasants have been buying up and consolidating their lands. That old fallback, running away to the big city, has been less of an viable option as cities try to struggle with their own poor and unemployed and take steps to discourage new arrivals. The burden became too much to bear in the 1590s, which saw widespread peasant revolts. The largest was the rising of the "Croquants" in the Southwest in 1594. Henri IV was sympathetic to their suffering, saying that if he were a peasant, he’d be a Croquant himself, but the revolt was eventually suppressed in the usual way and the leaders executed.
Except in the Southwest, most of the peasants remained Catholic throughout the wars. For one thing, there were about 100 religious feast days a year, and they provided the only real relief from work most peasants got. This is in contrast to the urban merchants, who viewed holy days as a loss of opportunity to buy and sell and make money. Protestantism was much more popular among the mercantile class. (One of the terms of the eventual Edict of Nantes was that Protestants had to observe the Catholic feast days.)
In the cities, the artisans have also been affected by economic change. Their guilds, traditionally the most powerful corporations in most towns, have been losing ground to the emerging urban oligarchy of the wealthy neo-capitalists. Urban poverty is also a big social problem. However, new trades like printing have opened up new opportunities. Merchants and tradesmen in the new industries are more likely to be literate, and for a while, were more likely to be Protestant as well.
The major cities have been strongholds for the Catholic League, Paris being the foremost. Because the League advocated deposing a legitimate monarch, they ended up attracting political extremists that proclaimed that all power came from the people. The first barricades went up in the streets of Paris in 1588 (the beginning of a venerable French tradition). During the anarchy between the end of Henri III's reign and Henri IV's triumphal entry in 1594, Paris was ruled by "The Sixteen", a revolutionary committee of citizens that enforced the rule of the people through a program of terror. (The events of 1789 were never very far from the French soul.)
The chaos of civil war has meant that for the first time in centuries, commoners may find themselves in careers as soldiers. Since the 14th century, the nobility had considered it unwise to arm the common people. Most of the infantry used in France were foreign mercenaries, hired from the Swiss cantons or German princes. But the demand has been high enough to create a market for the native-grown variety. One noble commander lamented this trend, saying that a butcher's son might have an illustrious military career and be honored by the great as if he were the son of a duke.