There are two potentially relevant rules here.
The first is from Complete Arcane (p. 86):
Some weaponlike spells can strike multiple times in the same round. When the caster gets a bonus on damage with such spells (including sneak attack damage), the extra damage applies only to the first attack, whether that attack hits or not.
The second is from the Rules Compendium (p. 42, emphasis mine):
A form of attack that enables an attacker to make multiple attacks during an action other than a full-round action, such as the Manyshot feat (standard action) or a quickened scorching ray (swift action), allows precision damage to be applied only to the first attack in the group.
Some tables take the second rule to mean that, if your spell is cast as a full-round action, you can apply sneak attack multiple times. If you are playing that way, it is highly beneficial to use spells with casting times of 1 full-round action. The easiest way to achieve this is to cast spells spontaneously while modifying them with a metamagic feat (doesn't matter which), due to how metamagic interacts with spontaneous casting:
...because the sorcerer or bard has not prepared the spell in a metamagic form in advance, he must apply the metamagic feat on the spot. Therefore, such a character must also take more time to cast a metamagic spell (one enhanced by a metamagic feat) than he does to cast a regular spell. If the spell’s normal casting time is 1 standard action, casting a metamagic version is a full-round action for a sorcerer or bard.
However, this ruling is on iffy RAW footing, for multiple reasons:
- The Rules Compendium rule doesn't explicitly say that full-round actions can apply sneak attack damage multiple times, just that shorter actions can't.
- Published errata for 3.5 state that when rules conflict, "primary sources" have precedence over more general sources, and more specific rules have precedence over less specific ones. Complete Arcane seems more like a primary source for spell behavior than the Rules Compendium, and rules for weaponlike spells are more specific than rules for all actions.
The note from the guide quoted in the question appears to be saying that the author is convinced by such arguments, and does not believe that the Rules Compendium rule allows for multiple sneak attacks on a single spell.