This is a subject that I always completely geek out on and become a hyper-active 5 year old who ate too much sugar
Weapons/magic, how they work or interact and the rules they follow tends to be the most developed bit of anything I write, just because I can't help myself thinking on it.
I'll answer these based on myself as a reader and what I prefer to read.
A) How logical should be the most outrageous weapons?
This depends on the type of story you're going for. A spell that turns all enemy swords into jelly is something I'd expect in a fantasy parody world like Pratchett, or if the sorceror in question is a 13 year old sorceror in school who made up the spell cause it's funny.
If I'm reading a more serious fantasy/sci-fi novel I expect more logic to apply. A really powerful plasma cannon that can melt enemies, armour and all, I expect it to be an enormous two handed or vehicle mounted contraption that's extremely rare and very difficult to power with an excessive charge time. (A weapon like this makes an awesome plot point though, they need to rush the wielder before they can fire again)
Fantasy-wise, the same. Powerful spells take more out of the caster and take longer to cast. Or they come with a huge cost, like killing someone and using their life force to cast.
I don't mind outragerous weaponry, so long as it comes with a restriction of some kind.
B) Should the author know about the weapons and give a satisfying explanation to its working? [A laser rail gun, the size of a palm having a recoil that would throw a man away by a considerable feet (think MIB!)]
Again, I think it depends on the style of story. MIB was a parody of sci-fi movies, intended more for comedy than serious science, so no explanation was needed for the Noisy-Cricket. But that weapon would seem much more out of place on Star Trek, which often places more upon scientific explanations.
When reading a book I'm much more interested in internal consistency than I am with it being true in the real world. I don't mind if the weapon wouldn't work with our physics, so long as it makes sense in the story. If the story is based on our world though, then I do expect a bit more realism in it, but without slowing the story down with deep explanations.
C) Should the weapons stay in the original side?
[Like the technology that is being used today}
I think weapons would depend on the weapon itself and its design. I can't see humans using a weapon designed for a four-armed 10 foot tall alien, it'd just be too huge and heavy. But neither can I see them using a weapon that uses a different power source than what they have. Laser rifles don't use bullets. Over time, like years, each side is likely to acquire bits of the other sides technology and make advances
In a fantasy world, general weaponry would be used by whoever. Magical stuff can have restrictions on it. Why yes you can wield that magical sword, but it won't cut anything as you're not the owner.
D) For fantasy, you don't go beyond swords and maces. So what is the boudary in creating weapons for Sci-fi and fantasy?
Depends on the world. You can go beyond swords in fantasy if you wish, add a group of people early into gunpowder weaponry. Steam-powered tanks (like Warhammer's Empire army).
Actually I think magically empowered guns could be pretty cool. Machine guns that shoot magical energy not bullets, and you place a rune upon the weapon to determine what it fires, be it fire or explosive or ice shards.
Boundary on sci-fi... I was going to say when you've destroyed reality, but I vaguely remember a story that's plot point was the destruction of time and every version of reality, effectively destroying every universe. Might've been Spiderman. Yes, it was, Spiderman the cartoon. Spider-carnage was going to destroy everything.