What you're really asking is, "is +1d6 elemental damage better than another +1 Enhancement?"
An Enhancement bonus adds the following:
> +1 to attack rolls
> +1 damage on hits
> +(M-1) damage on critical hits (the +1 multiplies on a crit, while +1d6 doesn't)
> 3E: (+1 to HP and +1 to Hardness of item). 3.5E: (+10 to HP and +2 to Hardness)
> 3E: (Cannot be sundered by a weapon of lower Enhancement bonus). This isn't in 3.5E.
> 3E: (Bypasses higher DRs). This isn't in 3.5E thanks to the /magic DR.
Even ignoring all those later ones, +1 attack and +1 damage that multiplies on a crit compares fairly well to +1d6 (ave 3.5) elemental damage, to where it's just a matter of taste.
Take the Power Attacking fighter. +1/+1 converts to +2 damage (+3 if you're using 3.5E and a 2H weapon), not counting crits. But, as many Power Attack treatises have shown, in most cases you don't WANT to Power Attack, even without considering crits. If you'd do 40 damage per round (assuming all attacks hit), but only hit 50% of the time, an extra +1 to your attack means 2 extra points of damage on average.
Also, in many ways attack bonuses are more valuable than damage bonuses, because you can't trade the other direction. An attack bonus can be traded for AC (Expertise/Fighting Defensively), damage (Power Attack), etc., but how do you INCREASE an attack bonus?
Then there's all the stuff that activates on hits. If you've got Sneak Attack dice, you just want to hit at all costs.
Then there's the DR/resist issue.
Let's say you picked Flaming. If the target has ANY Fire Resistance, all 1d6 damage will probably be lost. If the target has DR, the only way the extra +1 damage would be lost is if you failed to power through the DR, in which case the entire weapon is useless.
In other words, the only situation where the Flaming is MORE likely to be effective is if the target has a very high DR that you can't breach, but has no fire resistance at all. In that situation, you're reduced to doing 3.5 damage per attack period, which probably isn't a productive use of your actions.
So, which is better overall? It really depends on what you're fighting. If it's stuff with very low AC and no elemental resists (like most NPCs) and you're only getting the single attack on them, the Flaming is better. If it's stuff with high AC and elemental resists (like a demon or something) and you can Full Attack, the Enhancement is better. Overall I'd probably go with the Enhancement bonus, since at high levels you're going to run into much more of the second type.