My human PC has been forced to assume magically the form of a typical squirrel, and his gear has melded into this new form. Does this melded equipment still have weight? If it does still have weight, should that weight be added to squirrel-me's body weight, or should squirrel-me be considered carrying that gear, probably making it so squirrel-me pretty much can't move?
If you were in medium or heavy load from encumbrance before transforming, you continue to take those penalties in your melded form. Otherwise, ignore the weight of melded items and calculate your encumbrance in your polymorphed form entirely based on non-melded items.
...if you gain no benefit from the melded armor, you still count as wearing an armor of that type, but you do not suffer its armor check penalty, movement speed reduction, or arcane spell failure chance. If you do gain any benefits (as with the wild property), then you do suffer the armor check penalty, movement speed reduction, and arcane spell failure chance.
So only if you gain a bonus from having the equipment melded do you count the weight. One additional note from Transmutation- Polymorph:
If your new form does not cause your equipment to meld into your form, the equipment resizes to match your new size.
So any weighted equipment would be a fraction of the weight as well.