You could probably base most of that list off of MM2 and MM9. MM6's weapons were really not that good.
Mega Man 9's weapons would be a bit more difficult for me to pin-point through a best/worst list. All of the weapons from that game are really good. It's obviously a lot easier with a set variety to the weapon's overall usefulness, such as the case with Mega Man 2.
Since I have nothing better to do with my time however, I may as well jot down my thoughts on each weapon - starting in order from best to worst.
[spoiler]
Metal Blade - I don't think I need to comment on this weapon, or how predictable it is for me to put it at the top of MM2's weapon listings.
Quick Boomerang - A bit of a difficult choice between this and the Time Stopper for the second place. While most people tend to play Flash Man's stage before Quick Man, the latter's weapon is definitely more useful. With 224 total uses, and even with the aspect of rapid-fire, there's virtually no way to exhaust this weapon's ammo count unless you intentionally do so. This makes it all the more helpful for taking down things if by some chance you've gone crazy with your Metal Blade usage - which is a pretty good possibility, to say the least.
Time Stopper - While nowhere near as good as Bright Man's version, it's still a decent support weapon that has its fair share of uses in certain sections of the game. Quick Man's force beams not-withstanding, of course.
Air Shooter - Not the most helpful or direct of the weapons, but it can be used to instantly destroy those brutally annoying ride-mechs that some of the Sniper Joe's have acquired in this game. Other than that, Crash Man, and maybe for enemies that are above you, it doesn't have too many other uses.
Bubble Lead - While somewhat lack-luster at first glance, I actually find this to be a semi-decent weapon. Yes, there's a good chunk of enemies that it doesn't work on, but there's also a fair share that it's capable of dealing with just as well. The annoying Springer enemies come to mind on this.
Atomic Fire - This weapon doesn't nearly live up to its cool name-sake. The standard attack is pretty weak overall. The charged version, while obviously much more devastating and accurate in attack strength, is still agonizingly slow. By the time you fully charge this thing up, you could have used one of several other methods to deal with whatever you're planning on destroying with it.
Leaf Shield - The first shield weapon of the series if I recall, and it's also one of the worst. It has 9 total uses, barely protects you from anything without flaking out, and there are good number of enemies that it's absolutely ineffective against.
Crash Bomb - My disdain for this weapon seems to know no bounds. I think a part of it is due to the fact that the game forces you to use just about all of it for that stupid Boobeam Trap boss. Aside from that, the weapon itself is a mess. It has 7 total shots, is rather slow when being fired off, and has an unnecessarily long start-up time for its explosion. Aside from breaking the occasional door, and the aforementioned Boobeam Trap, this weapon is absolutely horrible.
[/spoiler]