You have the scroll tables. Use them.
1d3:
1: Standard Rod of Wonder effect; roll the 1d100 for the effect, run as normal.
2: Roll 1d10-1 for Arcane spell level, roll up the spell with a 1d100, and see below.
3: Roll 1d10-1 for Divine spell level, roll up the spell with a 1d100, and see below.
When you get a spell, you roll a few extra dice....
1d3: Spell Target
1: Spell targets the wielder.
2: Spell targets whatever the rod was pointed at (regardless of range).
3: Spell targets a random nearby location/creature (chosen by wherever the DM thinks would sow the most chaos).
1d3: Spell option control (Special: Wish and Miracle type effects only affect the target from above directly, regardless of other wording; Summon and Calling type effects put the critter adjacent to the target from above - but the one selected with this die controls actions when the spell duplicated says actions are controlled):
1: Wielder chooses any spell options
2: Whatever the rod was pointed at (regardless of range) chooses any spell options.
3: Random nearby creature (chosen by whatever the DM thinks would sow the most chaos) controls spell options.
1d20: Caster level (even if not normally possible - you can have a caster level 1 Weird).
1d20-1: Effective ability modifier (yes, that's Modifier - you roll a nat-20 on a cantrip, the save DC is 29; you roll a nat-1 on Wish, the save DC is 19).
Oh - and the DM rolls all dice behind the screen. If it's a Wish, the DM asks the selected character what he Wishes for - not telling him the caveats or who will be directly affected. If it's a Summoned Monster, the DM lists off some creatures and asks the selected controller to pick one. If it's Lesser Planar Binding, the DM asks the controller to name a 6 HD or less outsider or elemental - and so on (do note that with the Planar Binding line, the Caller only gets to negotiate and control if the appropriet bindings are in place....). If it's Protection From Energy, the DM asks the controller to name an element. And so on. The DM then grins evilly and speaks for what the wand has wrought.