I was thinking about weapon speeds...
Generally speaking swords are faster/easier to swing, than an axe, which is in turn easier to swing than a hammer, etc.

So in 3.5 are there any rules that take this into consideration. Say an opponent using a sword against someone using an axe, would get an attack of opportunity every third swing or something.... to account for the different weapons speeds?

Official rules off the top of my head? Nope.

There are feats which sorta emulate it based on weapon type but nothing to do with speed per se.

I have yet to see something like this as a standard rule, but there are some instances where you can make an attack roll against an opponents attack roll to parry it, or the rogue special feature where you can make a reflex save to deflect the attack and take half damage if it were a lethal blow. There's also deflect arrows, which lets you do it for shots coming at you.

But, I rant. There isn't a rule that takes in to effect the heaviness of weapons, as the game assumes most people who are wielding said weapon have taken the appropriate training to use it as well as anyone can use their own weapon.

Double attack I guess? Since you can't use two handed weapons quickly, it's not really that good. You could also just describe your one attack over the given attack as multiple times, for the same damage. It would then be just a cinematic difference, so you count the damage the same a single attack.

2e edition had this, a weapon's speed factor, the various weapons adding different modifiers to your initiative roll. You could probably just adopt that model if you want that kind of realism in your game. Though, having played both, I prefer the stream-lining in 3.5 in this regard.

Does 2e? I don't recall that. But then it has been YEARS since I actually played 2e.
I guess I should pull out my old books and actually read through them again.