Yeesh. Took you long enough. I've been waiting for a thread like this to pop up for months.
Standard Weapon:
Beam. It is accurate, it has the highest damage rate of any standard weapon, is very easy to hit enemies with, and encourages "ram-and-board" combat, my favorite style (missiles just aren't the same when they aren't hand-delivered to the cockpit of your enemy with a bow wrapped around them ).
For the others: Pellets have a decent damage rate and excellent range, but are hard to aim. Homing locks onto targets, but those targets are seemingly randomly chosen and the damage rate is bad. Wave is simply too weak and too narrow.
Super Weapon:
Super Wave. It is extremely powerful due to the increased fire rate and damage-per-shot, has a wide spread, and can hit large groups of enemies simultaneously.
For the others: Super Beam has incredible range and accuracy, but only hits one target at a time, and doesn't have any damage rate increase over the standard beam. Super Pellets have a very good fire/damage rate, and are easier to hit things with due to the bounce, but aren't quite as lethal Super Wave. Super Homing has a decent damage rate, but still locks onto semi-random targets.
Note that this opinion is based primarily on multiplayer play, which has a somewhat different style from single-player. On the other hand, a quick look at the high score list will tell you my multiplayer credentials.
Oh, and my favorite weapon color is green.
Edwards