Bad Guys are the villians of the story, whether the local thief's guild or some cultists trying to summon their dead yet sleeping god they mean you no good. What does this really mean though? Does being the bad guy mean your always evil and that you like to kick puppies for fun? No, where is the fun in that. If the heroes can just go and kill them and have the town praise them its generic. Let's add some spice to our bad guys!
What if the guy is only evil in your realm? What if in his home he's a nice guy and donates to charity? When the heroes storm his castle will the people celebrate, of course not, you just killed that nice old man who everyone likes. Now the heroes are bad guys to, at least in that kingdom. How will the players react when they find not joyous thanks but an angry town guard contingent waiting to arrest them after vanquishing the bad guy? That is if they just rush into it. If the players actually roleplay and find out that the guy is loved then they have to figure out what to do. Do they try to enlighten the town to his evilness first? Maybe they go the assassin route then get the hell out of dodge. There are all kinds of opportunity that open up when the bad guy is only selectively bad.
What if the invading army is only trying to get away form something worse? Do you blame the human barbarians when they invade because the orcish hordes are pushing them towards you? How do the players respond when they final get to the barbarian warlord for the final fight only to find a haggard man that is trying to save his people? What happens then, do the players now try to help the barbarians? They have been trying to invade for a while and all of the countries dislike them so no one wants to help them now. How do the players work this out because no matter what the orcs are still there and will have to be dealt with.
What if the evil wizard that the king sent you to kill is only considered evil because of political reasons? Yes you get a lot of money from the king if you do it but how will the mage guild respond? What if the players don't kill him, now they have the king angry at them! Maybe it was the mage guild itself that sent the players but the reason turns out to be unsanctioned magic use and not anything else? How do the players react to it when they find out that He just happens to be a different type of magic user?
Also bad guys don't need to have done anything evil, or bad, or even just something against the law. A king tightens his grasp on the peasantry to much can be considered evil even if he is not actually "evil" and may in fact be of Good alignment.. How do players get rid of someone who's only evil is greed, or gluttony? Maybe the king only likes his wines a little to much or maybe he gambles more then he should. He is still a good man but his actions cause evil. His constant consumption of rare wines needs to be funded somehow. His gambling away of things when drunk loses to many expensive things and taxes need to go up to replace important things. How can the players deal with this?
The king is the bad guy because of constant and heavy taxes starving the poor and such as well as allowing the thieves to much freedom because of the under staffed guards. None of this thing will change until you change the king whether literally or figuratively, but assassinating the king is not something heroes should do on a whim.
Anyway if you just kill the king then unless you prepare for it chaos. Just going and killing someone in a situation like this is never enough. The heir is probably just like his father and if there is no heir then all the people who feel they should be the new king will try to take over and the kingdom falls into civil war and savagery as it pulls itself apart at the seems. A good bad king can provide just as much if not more adventures as a truly Evil king.
Also there is no bad guy as bad as a player created bad guy. Has your group been wanting to try an evil campaign? Let them and when its done if any of the characters survive then you have a perfect start to the next campaign. Think of the reactions when they find out that their first level character's home town was razed by themselves. Just imagine how personal it will be when they find out that the guy begging for his life in that one place they barely remember is your new character's father.
This of course works best if you play in a persistent world and are not just starting over every time and they should be told that you may use their character in the world later but otherwise its a fun thing to do. Plus when they finally beat the evil characters there is more feeling of accomplishment. Kobolds are fun and all but they are only kobolds, but a player created bad guy is something that represents their ability and as arcades have shown we love to exceed our best and with DM created opponents you don't always get that feeling. It is considerably more so now then in the past. D&D 3.5 is a fun set of rules to play but the way it is set up is so that you only fight challenges you can beat, while a player is not under no restraints on their min-maxing ways.
I am not advocating that you go and create a game where no one is actually "evil" or "bad", just that you don't need to always have the absolute bad guy of evil evilness. Throw your players for a loop once in a while and see what comes out of it.