Alternate Form and Stacking
Rules of the Game has examined stacking magical effects before. That series, however, dealt mostly with the rules regarding combining bonuses from magical effects. Changing forms tends to be a little less straightforward.
The rules on combining magical effects on pages 171 and 172 in the Player's Handbook contain the key to handling an alternate form's interactions with other magic.
Alternate form doesn't provide any bonuses or penalties to combine with other magical effects -- it works changes that alter the user's physical attributes. Any magic that provides a numerical bonus or penalty affects a creature in an alternate form normally. For example, a bull's strength spell works on a creature no matter what form it's in. If a creature receives a bonus, such as an enhancement bonus to an ability score, before changing form it retains that bonus when it changes form. Just apply the bonus to whatever basic attribute the new form provides. For example, if the creature changes into a troll, it gains a Strength score of 23. If it also has a +4 enhancement bonus to Strength from a bull's strength, it effectively has a Strength score of 27 while it remains in troll form and while the bull's strength spell lasts.
Effects that work some sort of physical change on the recipient fall under the rules for effects that render each other irrelevant. For example, spells such as fins to feet and girallon's blessing from the Spell Compendium both transform the recipient physically (the former turns a creature's swimming fins or tail into motive legs useful on land, the latter spell causes the recipient to literally grow an extra set of arms). Since a creature gains the assumed form's body layout and limbs upon changing, the change in form makes either spell irrelevant. For example, if a creature using either spell assumes the form of a horse through alternate form, it becomes a typical horse, with four legs and four feet with hooves. If the creature later reverts to its original form, either spell still applies to the creature, provided the spell's duration hasn't run out.
It's worth noting, however, that the order in which these effects are applied is significant. If the recipient of a girallon's blessing spell has assumed the form of a horse, it grows two arms that end in claws (because a horse has no arms, see the spell's description). If the creature later reverts to its original form, it loses the extra arms (they belong with the horse's altered body).
