I, too, cried over Wolfwood' death and also Vash being forced to kill Legato. These were the two parts of the series with the most impact, IMO, because they are both turning points where both characters are realize that they have betrayed their ultimate convictions. Wolfwood, ultimately a good man, has to pay penance for his participation in the Gung-Ho Guns, something which he evidently comes to regret after spending so much time with Vash. And of course, Vash, who vowed never to kill anybody due to the wrath his brother unleashed and caused *him* to unleash with his plant gun. Vash and Knives are essentially Angels, though they aren't necessarily so in the classical religious sense. I doubt even the humans know where they come from specifically, but they are rather beings that just *are* as, say, the idea that God just exists and has always existed. Apparently normally benevloent creatures of great power, they have long lives and tremendous amounts of energy.
Most of these "Plants" are used to fuel the ships carrying the colonists and, later, to provide power and livelihood for the cities which spring up on the new planet's surface. Of course, due to the calamitous way in which the ships are crashed into the planet, much of the technology is lost and most people eventually forget what the Plants are or how they work - merely that they are crucial to the functioning of their daily lives.
Obviously, there are some general religious comparisons here.
Knives and Vash ultimately represent vague ideas of good and evil. One could almost say that Vash represents the ultimate good of heaven, while Knives is a fallen angel who represents an ultimate evil. However, neither actually represents and ultimate anything, because their lives, unlike the other Plants, have been directly influenced by interaction with humans. Vash learns to love and value life through Rem, while Knives learns to hate through the ridicule and abuse he experiences. What we know, though, is that both are capable of highly destructive power in addition to their beneficial power, and Vash continually faces inner turmoil over his ability to control what's inside him.
What makes this all confusing, and what I think turns some people off the series is that its essentially built *backwards.* There's a lot of foreshadowing in the beginning, hidden amongst supposedly "filler" episodes that can only be understood after having seen the second half of the series, and can be further clarified by reading the manga. So people expect one thing and then see Vash act like a goofball for 10-12 episodes and wonder what the hell people are raving about. Thing is, as you may have figured out, Vash acts like an idiot on purpose. How can anyone believe he's a destructive force when he seems so stupid? As evidenced in the first couple episodes, nobody can believe that Vash is the man that he is because he's not at all what people are expecting. This allows him to basically stay out of the limelight and try to keep to himself while rumors continue to fly about concerning who he is and what he actually looks like.
His goofball demeanor serves a second purpose, as well. As they say, humor is the best medicine, and its certainly the best way for Vash to deal with his own problems as well as with other people that he encounters. He'd obviously much rather keep his burden to himself, but as the series goes on, its something he seems to have a harder and harder time doing until he ultimately breaks down and shoots Legato. All of this is basically a way for Knives to prove to his brother that he is capable of the same kinds of violent acts as himself.
I already feel like I've written an essay, so before I go on too long I'll just wrap it up and answer a couple more questions:
1) The series does and doesn't answer many questions. :\ What I mean by that is that it certainly doesn't answer them directly, but with enough thought put into it, there's quite a bit of hidden depth. All the answers are essentially there, but many of them are inferred through a little guesswork. They don't just come out and explain everything.
2) Its really unknown whether Vash killed his brother or not. I think they purposefully left this open, but its ultimately assumed by most people that he didn't. Because he killed Legato and broke his oath doesn't mean he's willing to kill again. Knives wasn't able to convert Vash or make him feel superior to humans. Futhermore, why bandage a dead body? And, of course, if you watch their final duel, he shoots him in the arms and legs so he can't move. Totally incapacitated, and given Vash's convictions, its highly doubtful he would've shot him after he couldn't move anymore. What likely happens afterwards is that Vash gives him a nice dose of brotherly love and attempts to immerse him in a happier human society than he experienced as a kid.
3) Trigun has multiple refrences -
Vash's 3 guns: his pistol, the hidden one in his arm, and his Plant gun.
The trinity between Vash, Milly, and Meryl (of course this kind of goes out the window once Wolfwood shows up).
And I believe that Wolfwood's cross also has three firing modes.
There may also be other references here and there, but those are the ones I feel stand out the most.
