Here are some spell synergy ideas for several different spells.
Deeper Darkness could be used in synergy with Minor Creation or Major Creation to create a trap. The Creation spells do not allow for machinery, but there are many possible static traps, such as punji sticks, caltrops and trip wires.
Polymorph (self) can be enhanced with Union of Body. The latter is 6th level and I found it in Renegade Wizard's Spellbook from Mongoose. It allows two beings to merge for a short time. Two wizards using Polymorph can gain access to a lot of extraordinary abilities by selecting the right creatures while merging.
A couple more spells from that book are Shadow Fangs (5th level) and Web Bind (1st level). The former allows the caster to attack through shadows, sort of like the 1e boggle. The latter is a Web spell that only affects one target. Combined, they allow the caster to glue a target to a wall or floor and do so from hiding. A higher level version of Web Bind allows for multiple uses and would make a muc better spell for synergy.
Alter Liquid is a wizard spell is from Green Ronin's Advanced Player's Manual. It is a 1st level spell that changes any non-magical, non-harmful liquid into any other such liquid, but in small amounts. A 6th level version can be used in synergy with Control Weather to turn all the resulting rain into some other liquid, which can include some that are harmful. Though it does less damage, it is much more useful than Storm of Vengence as that spell destroys the landscape, affects a smaller area and is much higher level. Poisons that only affect orcs (or what ever monster), tanglefoot glue that only affects iron and lamp oil are just the tip of the iceberg.
Alter Metal is a 5th level wizard spell from the APM. It allows the permanent change from one metal to another as long as the result is not more valuable than silver and it solid at room temperature. A 7th level version should be able to affect mercury and other liquid metals. Combine that version with Control Weather and it can rain silver or other liquid metal.
In fact, Control Weather could be used with higher level versions of Cure X, Remove Disease, Polypurpose Panacea, Haunting Mists, Rain of Frogs, Fleshworm Infestation (those 4 are Pathfinder) and a variety of illusions to affect a large number of targets or increase the area of effect. It could even be combined with a 5th or higher level version of Create Water to increase the amount of rain to beyond hurricane levels. 20 feet of rain is more than enough to drown everything within the affected area.
