Here's a list of spells I think need to be house ruled to give mundanes a fighting chance.
Individual spell changes:
Celerity, Greater Celerity: Cannot be used to cast spells
Charm (Person, Monster, etcetera) spells give a 10+CL bonus on diplomacy checks with the affected creature.
Contact other Plane: You may ask only one question per week
Contingency: Contingency only works if the trigger condition involves the character or object attended and all trigger conditions must involves a state or effect on the attended entity, not one about to effect the entity. What that means is 'If I'm hit for damage then X' is valid while 'If I'm about to be hit for damage then X' is invalid. Only one contingent spell may activate in a round, if an action causes more than one contingency to activate the one cast is chosen at random.
Communion: This allows your god to tell you a message, by the time it gets to the prime material plane it may only be comprehensible as a riddle, or an obtuse quatrain.
Dimension Door only works if you have line of effect to the destination, or to a range of 50 feet
Freedom of Movement gives +20 to escape artist checks and to resist grapples.
Force Cage takes one round to cast
Genesis does not let you vary the flow of time on your demi-plane.
Glibness allows a will save.
Invisibility, Improved Invisibility and Superiour Invisibility take one round to cast
Iron Guard only works on Iron, not any other material.
Knock lets you use disable device at a distance, add your caster level to you disable device check
Mind Blank gives a +10 bonus to resist divinations
Moment of Prescience does not give a bonus on initiative checks
Scry and Greater Scry: You may see and hear at a distance as per Clairvoyance/Clairaudience, you may rotate the sensor in any direction and can move it at a rate of 60 feet a round. You may jump it to another destination once per minute. It does not work across planes and does not automatically find people, you have to specify a location your are familiar with. Scry's range is 1 mile per CL, Greater Scry's range is 100 miles per CL
Silence takes one round to cast
Solid Fog Only halves a creature's movement.
Teleport Can only take you to a previously created portal or mark
True Seeing has no material component and only gives a will save vs. illusions
Wraith Strike takes a standard action to cast, it lasts until the end of your next round
Wall of (Stone, Iron, Force) come into effect over the course of one round, characters can circumvent these by a reflex check. A character may attempt to attack or perform a strength check against one object as a free action once a round.
Miscellaneous
All spells that inflict a status effect must allow a save. If a character beats a save by 5 or more, or gets a natural 20 they suffer no effect from the spell what-so-ever.
Meta magic:
Divine meta magic and other sources of free meta magic do not allow you to cast spells of a higher effective level than you could normally cast. For instance a 3rd level Cleric could not maximize an inflict lesser wounds spell with divine meta-magic.
Negative Energy
A character will never have more than half their level in negative levels. A negative level applies a -1 penalty to every d20 roll. Negative levels from enervation go away after 1 hour, all negative levels are lost with 8 hours of sleep.