Best bets: Bags of Devouring, Sphere of Annihilation (watch yer dangly bits :o) or small portal to another dimension.
Hah hah yes portal to another dimension...
"You and your party arrive in this smelly cave. About thirty feet up you can see this pale blue glowing aura in a ring shape floating in the air. After a short while the ring glows bright - something is coming through. Everyone make a dexterity check..."
Nobody wants to put in a library? Admittedly, an individual's medieval-type library might be a few tens of books maximum, but it's still important. If your mage lives a long time it might well be hundreds or thousands of books.
The decor and features would be dependent on the specialty and interests of the individual. Someone specializing in sky magic might have many balconies and a wide, cup-shaped top to maximize sky access. Similarly, an earth specialist might have a strangely humped and conical "tower" with multiple bases to maximize earth contact.
The purpose of a tower is (historically) for defense and to impress the heck outta the locals. If you want to be a grossly over-magicked tower then the odds are good that there will be delicate spires or nasty spikes. Flames that ripple up the outside or clear blue-white light emitting from the joint area of every block. Elaborate gardens, vaulted entryways, reflecting pools, towers that float slightly off the ground, separate rooms, actual glass; all of these things are very impressive to the typical peasant and/or king.
I recommend the usual places to sleep, to work, to live, to study, to attend to bodily needs, and to relax. Note that with good transportation magic these places don't need to be in a traditional "tower" at all. It might be a collection of smaller areas in very different places. Is your mage an insomniac? Maybe there are a set of sleeping areas in different parts of the globe to allow for transit to an area best suited for trying to sleep when the urge strikes. Just brewed that potion of youth after being elderly? Maybe several of the gates go to places that the youth favor.
The most important accessory for the Ultimate Mage's tower is, of course, the Ultimage Mage.
Hookers! No, wait...um, I meant, an extradimensional space. Or lots of extradimensional spaces. I see those 20' diameter towers and always wonder how some double-digit-level archmage fits all of his stuff in there. Clearly they're larger on the inside than the outside. Any epic-level mage worth his bag of components is going to have a few pocket dimensions in his tower...good place to put the library, the treasure closet, the swimming pool (around which are gathered the HOOKERS!), etc.
All rooms as large spheres, with gravity always pointing directly at the 'floor'.
Why waste space!
A wizard tower shaped tardis.... hmmmmmmmmmm... has potential =P
I'd have minions, loads of em.
How about a teleportation device that dumps intruders at the front door or worse?
I remember reading a choose your own adventure style book when i was a kid, and it had an interesting trap that would fit in well in a wizards tower.
It was a elaborate pool. filled with what looked like clear water. In the center of the pool, under the water an ornate key can be seen, most likely the key that opens the door to the next room.
Upon reaching into the water for the key you grasp nothing, until the pool itself springs to life and attacks!!!
Basically the pool is home to a water elemental, which is invisible in the pool until someone gets close enough to be attacked... The mystery of the key is much simpler, and not at all magical. In the still pool an image of the key can be seen, but upon disturbance the reflection dissapates... thats right, a reflection. The key itself hangs from the ceiling, above the line of sight of the normal traveller. It'd be a good trick for those rival wizards, who would be trying in vain to find out what magics are protecting the key.
Depending on the wizards (and setting) perhaps a small chapel. Though wizards are not the most devout normally, many still worship a god, especially if they deal with summoning things