The PH should have authority on this matter. I think that spells with the harmless descriptor bypass SR if the target wishes, otherwise you have to roll. That is why the harmless is added to the saving throw and SR entries, to let you know. Look at Heal and Harm. Heal is harmless to living things, but not to undead. Here is the Errata authority clause:
Dungeon Master's Guide v.3.5 Errata
Errata Rule: Primary Sources
When you find a disagreement between two D&D rules
sources, unless an official errata file says otherwise, the
primary source is correct. One example of a
primary/secondary source is text taking precedence over a
table entry. An individual spell description takes precedence
when the short description in the beginning of the spells
chapter disagrees.
Another example of primary vs. secondary sources involves
book and topic precedence. The Player’s Handbook, for
example, gives all the rules for playing the game, for PC
races, and the base class descriptions. If you find something
on one of those topics from the Dungeon Master’s Guide or
the Monster Manual that disagrees with the Player’s
Handbook, you should assume the Player’s Handbook is the
primary source. The Dungeon Master’s Guide is the primary
source for topics such as magic item descriptions, special
material construction rules, and so on. The Monster Manual
is the primary source for monster descriptions, templates, and
supernatural, extraordinary, and spell-like abilities.
Dungeon Master's Guide v.3.5 Errata
Errata Rule: Primary Sources
When you find a disagreement between two D&D rules
sources, unless an official errata file says otherwise, the
primary source is correct. One example of a
primary/secondary source is text taking precedence over a
table entry. An individual spell description takes precedence
when the short description in the beginning of the spells
chapter disagrees.
Another example of primary vs. secondary sources involves
book and topic precedence. The Player’s Handbook, for
example, gives all the rules for playing the game, for PC
races, and the base class descriptions. If you find something
on one of those topics from the Dungeon Master’s Guide or
the Monster Manual that disagrees with the Player’s
Handbook, you should assume the Player’s Handbook is the
primary source. The Dungeon Master’s Guide is the primary
source for topics such as magic item descriptions, special
material construction rules, and so on. The Monster Manual
is the primary source for monster descriptions, templates, and
supernatural, extraordinary, and spell-like abilities.
