I second the liberal use of cantrips and spells in genereal and a strongly themed non-bland spell list. Crafting custom items and signature spells/items/tactics are also great. Also pick your feats to the theme, don't over optmize go for interesting flavour. For examples i clearly remember the paizo playtest chracters of Demon boy, a halfling sorcerer with the fire-dragon tbloodline feats, and the tomb born wee jas worshiping spellcastress who was herself very undeady.
Use the Valences model for spell levels to talk about magic in-game. Read Sepulchrave's excellent Story Hour for a glimpse of that. Sep also made use of very themed wizards who all stood out quite clearly from each other. His wizards were the rolemodel of what D&D wizards and their relations to each other should be. (Also much Jack Vance in there.)
A Spell Path system also works wonders for Wizards. Want to be able to tell one wizard from the others more? Give them different themes. Even if you don't implement the full spell path system use it to pick the different themed spells, I have always found the Spell Path System very useful for that. I've used the original 2E version by Kuntz/Baur from Dragon 216 quite a bit. A revised excerpt can be seen here: Spell Path Page
Sean K Reynolds adapted the basic system to 3E: Path Magic
And Green Ronin did an even better version in their Advanced Player's Manual, for their Eldritch Weaver class. The excellent Frilond site compiled an alphabetical list of spells and their Spell Threads and Spell Threads with spells from the Spell Compendium on their Eldritch Weaver Materials site.
I am very familiar with Sep's storyhour; the magic-users all have so mych flavor its disgusting

I really like the stuff on Spell Paths, it's very interesting work. The Eldritch Weaver cool, but I'm not sure if my DM would go for it.