If you stick to only using the Player's Handbook for spells, then you only really need to eliminate around 5 spells to create some extra flavor for your campaign..... Or, if you really insist on using many books with spells in them, remove 5 spells from each book.
What my list would look like, in a few incarnations (using 3E mind you, as I don't yet run 3.5E):
List A (removing most vast-distance, almost completely safe, nigh-instant-transportation)
1. Teleport
2. Teleport Without Error
3. Teleportation Circle
4. Etherealness
5. Shadow Walk
Dimension Door has a relatively short range, whereas Etherealness can cover vast distances with each casting and still bypass obstacles. Plane Shift is kinda unpredictable about where it deposits you on the destination plane, and it specifies that it transports you to another plane, and from the Material plane you can to go any other plane, so it cannot go from one point on the plane to another; you'd have to cast once to go to a different plane, then cast again to go back to the plane you came from, though you'd get to choose generally where to show up each time. Not nearly so instantaneous, on-the-mark, or whatnot as Teleport in most cases. Plus the focus component for Plane Shift is described as needing to be a certain type based on the destination plane, and may be hard to find at the DM's discretion, so it's likely the character would need a high Knowledge (the planes) check to know the proper focus for any given plane. One check per plane, really.
List B (simplifying the DM's/players' jobs)
1. Shapechange
2. Teleport Without Error
3. Discern Location
4. Polymorph Other
5. Polymorph Any Object
List C (preferred, removes screw-you spells that more or less can't be remedied/prevented/reduced/resisted well)
1. Mordenkainen's Disjunction
2. Enervation
3. Energy Drain
4. Harm (Feeblemind instead in 3.5)
5. Geas/Quest
Imprisonment can be avoided by simply not allowing anyone to learn your name, or using Illusions/Abjurations to keep enemies from finding out sufficient personal info about you. Two or three spells can locate an Imprisoned creature, and one or two can free them, and it requires touch to use. Power Word Kill can be avoided by simply keeping your hit points above 100 or casting Death Ward. Force Cage can be Disintegrated or, in cage form, escaped through all kinds of spells, like Gaseous Form or Dimension Door I think. Temporal Stasis requires touch, which like Imprisonment, can be avoided by simply going incorporeal or ethereal with a readied action. Polymorph Any Object requires touch, and cannot affect incorporeal or Gaseous Form stuff. Maze can be Plane Shifted out of, and high-Intelligence characters can find their way out in a few rounds otherwise. Most Symbols allow a save or are limited like Power Word Kill only moreso, and can generally be removed with the Erase spell. Otto's Irresistable Dance is thwarted by Mind Blank, which is the same spell level, and can be Greater Dispelled otherwise, plus it requires touch. Other stuff can generally be avoided, lessened, or dispatched with either Mind Blank, Break Enchantment, Death Ward, Greater Dispelling, or simply a saving throw. Some of the above, and some on my list, are lower-level than these countermeasures and thus impossible to negate/prevent/lessen when likely to be encountered for the first few times.
