- Spellcasting Levels: Not all wizard prestige classes continue spellcasting at each level. Wizards are all about spells and high caster levels. It's like reducing the fighter's BAB or the rogue's skill list. You can take a mild hit in favor of a great ability, but not more than one or on rare cases two levels. Greatly consider this before taking the level.
- Feats: Since you are already losing the wizard bonus feats, you are actively optimizing if you prestige in a class that offers bonus wizard feats. Be careful on the requirements though.
- Saves: There are classes that give you bonuses to saving throws different than those of the standard wizard. Remember that if you are multiclassing in a class with strong will and its rest saves are bad, you may take a hit in your fortitude and reflex on the long end.
- BAB: While not important, some prestige classes out there may provide you with average BAB. If you regularly use rays, try to prestige out of wizard at a level that can be divided by 2 (e.g. 6, 8, 10..). The main reason for this is that wizards receive their bonus BAB at that point. So a 5 wizard / 5 prestige will have 4 BAB if they both have a bad BAB progression, but a 6 wizard / 4 prestige will have a BAB rating of 5.
- Skills: Wizards are good with skills on average, so it isn't bad looking for prestige classes that expand their skill lists. The amount of skill points received is of course not that much important.
- Weapon Proficiencies: This shouldn't be the main reason of prestige class acquisition, but as an icing on the cake.
 Links to lists of Prestige Classes
The Complete Set