In addition to Complete Mage's elemental-themed heart of spells, that book contains the revenge-themed karmic aura, backlash, and retribution spells and the I-don't-have-to-tell-you-how-they're-themed unicorn blood, heart, and horn spells.
Complete Mage also includes at least one spell that works better when the target's affected by another, obviously similar spell: the 2nd-level Sor/Wiz spell escalating enfeeblement [necro] (CM 103) works particularly well on creatures already affected by the 1st-level Sor/Wiz spell ray of enfeeblement [necro] (PH 269).
In addition to the aforementioned dragon-themed primal spells, Dragon Magic contains the alignment-themed soul of anarchy, light, order, and shadow spells; two complementary ones can combine for greater effect.
Complete Champion contains the woodsy-themed forest child, eyes, and voice with the first spell being better if the second and and third are already active.
Fiendish Codex II's investiture spells grant fire resistance that explicitly stacks with the fire resistance granted by other investiture spells. It ain't much, but it's a thing, I guess.
Undoubtedly, I've missed some, but you can probably find others by looking for repeated first words. Authors seem to like to arrange these pretty consistently by repeating the first word so that when alphabetized such spells are conveniently located near each other.