It all ties together...
I do not tailor treasure or encounters. I won't repeat what others have said justifying the use of the random tables, but I agree with them.
If you design an adventure or encounter that makes sense, has a purpose and is internally consistent (why does this tribe of kobolds live here, who are their rivals, and how would they react to various situations), then it is 'believable'. If you consistently use the EL guidelines and tailor everything to the party, the campaign will be like a poorly written, predictable novel.
If the party makes poor decisions, they should have a situation that goes poorly for them. If the party makes a frontal assault on a cave complex that they have no explored well, they should not be shocked when, over ten rounds, over 70 kobolds swarm the area, many with various character levels (favored class: sorcerer).
This being said, I tend to structure the treasure to match the adventure. I break an adventure into logical chunks (for example, three factions of a kobold clan), figure the EL for the whole thing, and use the random tables in the DMG. The only adjustment I might make is deciding whether or not to adjust the EL by a slot or two in either direction, based on whether the chunk of the adventure was a wealthy or poor faction. If they are completely indigent, then I'll reflect that in their equipment, the general condition of the lair, etc.
The only time a place a specific item, it is because of the adventure plot. If it has anything to do with a character's choice of weird weapon, it will be purely coincidental.
As a player, I tend to play characters that are generalists. I include fighters in that. As a previous poster noted, a fighter class ability is proficiency with all martial weapons. I will not take any feat that requires a weapon choice until 9th or 10th level. There are enough good feats that it is still hard to choose, even if I don;t waste feats.
There is a fighter character in the campaign that I DM that has weapon focus with short spear. She has not seen one since she created her charaacter, and the chances of me rolling one on the treasure tables is infinitesimal. Certainly a wasted feat. Even if she took longsword, but later found a "+1 short sword of laying waste to entire regions", it would have been a wasted feat. Not even the fighter gets so many feat that he/she can afford to waste even one. It is just like a sorcerer picking a really stupid spell (permanency, for example).
I drifted a little OT, but it all really ties together. Do you want a programmed, predictable video game, or something that has the random chance of real life. Yes, majoring in forestry in college is cool, but you are more likely to find a job with an electrical engineering degree (no, I'm not an engineer; I made a similar mistake...).
-Fletch!