I read some where that there are not that many powerful bastard swords in the game(unmodded version).
So what are the weapon categories with the best weapons?

If I remember correctly, the best weapon is a Greataxe +5 (availiable only in HoF mode). Axe is generally a very good category, giving you access to one-handed, double-handed and throwing weapons at the same time. Also good are longswords, halberds, and hammers.
Using double-handed weapons gives you an additional STR bonus, but I think there aren't too many really great double-handed swords in the game, so I'd stick with axes/halberds.
Anyway, under 3rd ed rules, raising your weapon feats doesn't give you additional attacks per round, but just an attack bonus, so it's no problem to use weapons for which you only have one point of feats.

Ironside is right.
Axes come first. He is talking about the Massive Greataxe of Flame +5. No one seems to ever have found it ingame however. :bang: random drops :bang:
Maces and polearms are the other good weapon choises.

And if you have a Paladin, longsword for the Holy Avenger.

Ironside and Shirkant are totally correct, axes are the weapon of choice. I even have my cleric tank spend a feat on axe proficiency just so he can use them. Even without random drops like the Massive Greataxe of Flame, always available axes are excellent: Big Death (throwing) and Widow-Through (2-handed) are a powerful combination.

2-handed swords ain't bad. There are a few great ones (+5 vampiric or something) available at the Hand. Before that, Sherincal drops a nice human slayer.

Agreed, Sherincal gives a really nice gift for the Ice temple. Generaly, all of the enemies inside are humans, except for wolves, golems and trolls&shield guards.

As any fighter class gets a proficency in two-handers, it takes no effort to use it.

For two-handers, you need two things: big STR and big CON. You need big STR to make use of the X1.5 STR modifier and you need big CON because your AC will be affected negatively by not using a shield. Don't forget about Cleave and possibly even Great Cleave to make use of the extended range. It would be a waste to skip on Improved Criticals with this kind of damage and potential number of free attacks per round.

So far as specific weapons are concerned, apart from two-handed swords and axes, there is a number of pretty nice halberds. They also make one category with spears, so it's pretty economic to have Focus and Specialisation in polearms.