I don't think that your analysis of the bonuses and penalties really adds up.
As others have pointed out, a +3 sword with a -1 attack penalty isn't the same as a +2 sword. It has more hardness and hit points as they pointed out, but... there are some other effects:
1. It deals slightly more damage. +3 longsword with -1 attack penalty is d8+3. A +2 longsword is d8+3.
2. However, a +2 sword can be greater magic weaponed up to +3 or beyond and, at that point, the +3 weapon of legacy is just an indestructible sword with an attack penalty.
So, the attack penalty/enhancement bonus difference cuts both ways.
What doesn't cut both ways, however is the save penalty.
A sword that gives you a +3 resistance bonus to saves and a -2 penalty to saves is not giving you a net +1 to saves. Why not? Because, ordinarily, a PC would try very hard to get some kind of a resistance bonus to saves--a cloak or resistance or a vest of resistance or something. Otherwise, it is very difficult to make the saves that high level monsters and spellcasters generate. (For instance, Libris Mortis's Angel of Decay is a CR 14+ monster that requires everyone within ten or fifteen feet of it to make a reflex save (DC 25+ I don't remember whether it was 25 or 28; let's use 25 for the sake of this example) or take some damage as bits of the angel fall off on them and cause their flesh to decay and then, if damaged, to make a will save (the same DC) or be nauseated. In order for a 15th level fighter to combat the creature, he needs to make one of the two saves. Since they both start out at +5, if he had to rely upon class based save bonusses, he'd only be acting (1-.95*.95) of the time. However, let's assume that our 15th level fighter has a +3 dex bonus and a +1 wisdom bonus as well as iron will. Now, he has a 20% chance of making either save for a total 36% chance of acting in any given round. Mr. Fighter is going to die. Now, let's assume Mr. Fighter has a +5 cloak of resistance. He's 15th level, so he should. Now he has a 45% chance of making either save and a 70% chance of acting in any given round. Not too shabby. But drop that save bonus by three points and he's only got a 49% chance of acting in any given round.
At high levels, save DCs are high enough that penalties to saves are FAR FAR more dangerous than any resistance bonus the items might confer. Saying that the net effect of the item is +1 to saves is not meaningful because, under normal circumstances, PCs would have be using resistance items anyway.
There is a second effect that plays out in Merrick's analysis of the bow of the black archer. As he says, it's not a weapon anymore--it's a freedom of movement item. That may be so, but its bonuses also tie up a lot of its value in the weapon functions of the item. If an archer PC would, at that point, prefer not to use it as a weapon, then all of that gold is going to waste as the PC has to buy a different bow and use it.
But maybe you'll say that every PC doesn't have a +5 resistance item at 15th level and might be happy with a net +1 to his saves from items. And bow using PCs don't all want +1 flaming holy bows of seeking; some of them would be happy with a +5 drow-bane bow that beats any DR a drow might have (an ability that would be a lot more impressive if drow normally had DR--unless I misread my Monster Manual, they have to get DR the way any other classed character might which means they usually won't have any and when they do have it, they won't have much). However, I think that exposes one of the flaws of the WoL model: they're effectively suites of disparate abilities, only some of which will be useful or desirable for any given character. (I know the elven archer cleric of Shevarash I played for a while wouldn't have had any use for any of the bow's abilities other than its weapon and freedom of movement functions).
To drive home this point, here's what her take on the 20th level abilities of the bow would be:
20th level: 45500 gp; -2 attack; -3 saves; -16 hp
* +4 drow bane longbow
So, you're telling me I'd be killing more drow by taking the ordinary longbow I bought at 2nd level and casting greater magic weapon on it? (base rapid shot attacks for a 22 dex, 18 str (+6 belt and gloves) cleric 20 with no spells up = +24/+24/+19/+15 for 1d8+9 with an ordinary mighty bow and greater magic weapon or +21/+21/+16/+11 for 1d8+8 with the bow of the black archer (assuming its strength scales to the wielder) or +23/+23/+18/+13 for 1d8+10+2d6 vs. drow). This is supposed to be the weapon of my god?!? Where can I ditch it for an ordinary +1, elfbane bow?
* +3 insight bonus on Will saves to avoid mind-affecting and compulsion effects
Very nice--but it doesn't come close to making up for the -3 I take on all saves and against all effects.
* at will - detect drow
A rather marginal ability if it functions like Detect Evil and I need to concentrate to do it.
* ignores drow's damage reduction
Oooh. So which drow have DR again? Usually I'd just use adamantine arrows on drow who cast stoneskin....
* 1/day - darkvision, shadow walk, arrow of slaying (drow)
I could get behind the arrow of slaying, but ordinarily I'd just cast daylight or windwalk or word of recall for the other two abilities--they work better.
* 2/day - lesser restoration, protection from evil
Tell me why I'm supposed to be impressed to save a 2nd or 3rd level slot again?
* 3/day - longstrider
For what, running away faster because I'm wielding a bow that doesn't help me kill drow?
* 5/day - imbue arrow with 5d6 electrical damage as standard action
Oooh, so I can give up my four attacks that would each deal 1d8+11+2d6 to drow (avg 22.5 damage) to add 17.5 average damage to one arrow that I have to shoot in the next round. When can I start? And how can I get a full draw when pointing this bow at my foot?
* continuous - freedom of movement
Nifty. At least the bow has one ability I'll use. (Though I could get the same effect by using up most of my 4th level slots and would ordinarily just do that instead of getting a ring).
* base landspeed increases 10 feet
Spiffy. I wouldn't pay for it, but I won't complain if it's free.
* +5 competence bonus on Hide and Move Silently checks
Since this brings me to a grand total of +11 to each at 20th level, you'll pardon me if I don't jump up and down in joy.
My cleric's analysis: Two thumbs down: WAY down.
The costs offset the costs of these functions that PCs will often neither desire nor use with penalties to abilities that PCs both desire and do use. The net result is that, as a friend of mine whose character had the misfortune to receive a WoL in another campaign said, PCs who find them will be better off without them.
