There's some mentions of what changed in the mentality of the guilds in the "Best of Guilds" threads.
What changed with the Dark Brotherhood is that Sithis was not present in Daggerfall. Members would not always praise Sithis and say "Go kill him for Sithis". So they seemed to perform their assassinations only for the benefits of the Brotherhood's pockets.
As for missions, they mostly involved assassinating former members of the Brotherhood, noble knights, mages, war veterans and even high-ranked Thieves Guild members.
Interesting to note for the Dark Brotherhood, the contract for involving the assassination of a rogue mage had been given to the Dark Brotherhood by the Mages Guild. So even the noble Mages Guild uses the Dark Brotherhood to kill traitors to their guild.
In Morrowind, I believe that's where Sithis was introduced. They've never changed, really. They are still a guild of professional and not-so-professional (In reference to some of Oblivion's guild members) who kill for Sithis and for gold, wheter it's a contract to assassinate a criminal or a child.
The Thieves' Guild radically changed. In Daggerfall, it's truly an organization of thieves, rogues, ruffiands and prosttutes who control the criminal activities of the cities and regions they are present.
They capture children for ransoms, control the smuggling business and they are not afraid of sending though guys to "dispose" of freelance thieves who dare threaten their business.
In Daggerfall they are a bit more harsh and direct, while in Morrowind they are in-between. On one side, you have the Bal Molagmer quests where you steal from the rich and unjust to give to the needy, while on the other, you get missions to steal precious gems and riches from nobles for the profit of the guild.
In Oblivion, it's the Gray Fox and his band of Robin Hoods. Steal from the rich, give to the poor. They don't seem to really control the criminal activities in Cyrodiil.
Also worth to note is that in Daggerfall and Morrowind, most of the citizens knew that the Thieves Guild existed. Even guards didn't deny it. In Morrowind, some even pointed you to where they were hiding out.
In Oblivion, for some obscure reason, the guards will deny its existence and tell you that you're crazy minded to ask such things. "It's impossible, can you imagine a gang of thieves trying to run a guild!?"
Some of the citizens seem to deny it as well. Which doesn't make much sense since they've been in the history of Tamriel for a very, very long time.
Fighters Guild. In Daggerfall they were simply your usual mercenary guild to call for help when you have monster problems. Rats in your bed, spiders in your cabinet or giants in an old property of yours. Actually, every single quest of the Fighters Guild implies a creature of some sort. So they didn't have a specific point of view on things. Very bland actually.
In Morrowind, it gets interesting because the higher ups were corrupted by the Cammona Tong, Morrowind's equivalent of the Thieves Guild. The guild master, his associate and one or two guild hall leaders were paid by the Cammona Tong to kill certain outlanders who were, I suppose, endangering the Tong's business. Those individuals apparently "had a bounty on their head" and, so, they needed to be slain. By making it a Fighters Guild contract, the Tong could continue their usual activities without having the law knocking at their doors for performing murders.
In Oblivion, the Fighters Guild had a strong and un-corrupted leader. Which is why they were on the good side of the law in every way. They were not in good terms with the Blackwood Company, of course, but only proceeded to go against them when enough proofs were gathered of Blackwood's criminal activities.
Mages Guild, I'm afraid I can't say much. I never played through them in Daggerfall and only barely in Morrowind.
But from what I played and read, the Mages Guild always love to "dispose of" former members who decided to become traitors.
In Oblivion, they had an very poor leader (Arch-Mage Traven) who basicly lead the Mages Guild to hell. Banning Necromancy as his first Arch-Mage decision, which has been legal since the Mages Guild existed, was not a good idea. If half of the Council of Mages resigned, I suppose half of the guild members did as well, preferring to join Mannimarco's Necromancers than being persecuted by their former boss. So it lowered the ranks of the Mages Guild and greatly helped Mannimarco gather forces. Bad idea..
Then Traven restricted access to the University. Taking this decision after having cast out half of the Mages Guild surely didn't help them having full-fledged mages.
Oblivion's Mages Guild spoiler:
Spoiler Oh well, at least he's dead now. Hopefully, the new Arch-Mage will do a much better job than Traven.