Using a prestige class in an older style game is easy. Have an entrance requirement. This triggers the drawbacks and restrictions. Then the character may split experience points between his two classes as he wishes.
10) Thief: If you're going to take the thief as a class, perhaps it works best as a prestige class. This may in fact have been the original intent. If you're going to have it, allow players to dump experience into the class to acquire the skills, at the expense of their primary class.
9) Assassin: This is a fantastic prestige class. It has an entry requirement of killing someone for money. It gives basic thieving skills after a level or two along with the ability to use disguises and poisons. It lacks the ability to disarm magical traps and locks. Also allows the character to raise money by committing murder for hire in their free time. Class abilities can be lost if anyone discovers your true nature.
8) Paladin: Real holy power in exchange for a little tiny moral leeway. This prestige class is a bit more stringent then the others, replacing fighter classes only and preventing improvement in the original class. It also comes with a number of moral imperatives depending on the god along with an annoying vow of poverty, but the holy powers of laying on hands, detection of evil, protection from evil, being able to use holy swords and mounts provide power to make up for the restrictions.
7) Mystic Theruge: A spell caster who's interested in magic from all sources, not just wizard or cleric spells. Possibly available from rare temples or places in the wilderness. Each level taken in this grants new spells from a variety of magical traditions, such as druidic, wizardly, clerical or even stranger magical traditions. Working with such arcane energies is very physically taxing and often will cause strange deformations in those who break such natural boundaries that way
6) Necromancer: Because all the spells for death shouldn't be assigned to different classes. Of course your close association with the dead brings attention you would rather not have. Also odd smells. Also bargains with the dead tend to imperil your soul. On the plus side, undead servants don't complain when you use them to set off traps.
create history, and add skills, and still allow the character to advance normally. Time spent among a pirate ship can give a basic proficiency at all ship related tasks, bonuses on ship to ship combat, skill at fighting on rigging and moving across vertical surfaces quickly, mastery of mounted shipboard weaponry (such as cannon), and an increase armor class and breath weapon/wand saves in light or no armor based on their level. Surprisingly useful when your ship suddenly takes off into space.
4) Magical or Martial Speciality: This prestige class takes a specific magical or martial style, like gladiator, elementalist, pyromancer, or Cavalier and provides additional abilities. Sometimes players want to have a specific focus, and using prestige classes in this way allow the DM and the player to work out how that happens mechanically. This is useful for when the natural customization options of flavor and class don't provide abilities the character seeks. Some sacrifices, limitations, experience point expenditure and in game effort later and they can give up normal advancement for some of these abilities.
3) Beastmaster/Rider: Fiction abounds with the bond between characters and their pets and mounts. Adding a little mechanical benefit. Spider-rider, Dragon-friend, Worm-rider.
2) Cultist: Because if the party is going to be fighting them, shouldn't they have some unique abilities? And then you're more prepared for when the party eventually wants to join them.
1) Ninja: But not at my table.