Immediate and Obvious Steps
Full Base Attack Bonus
Between their low HD, weak weapons, the penalties that Flurry of Blows applies, and so on, the less-than-full BAB of the Monk is just insulting. Switching Monks to full BAB is probably absolutely necessary.
Magic Unarmed Strikes
Allow Monks to upgrade their Unarmed Strike as a magical weapon. Charge 300 gp for “Masterwork” quality (and the +1 Enhancement bonus to attack), and then (enhancementBonus)²×2000 gp for additional bonuses.
As a DM, if you don’t want to just outright houserule this, a magic weapon that uses the value of one’s Unarmed Strike damage as its base (a magic gauntlet, perhaps) may fit what you’re looking to do more.
Another Pretty Good Idea: Armor
Allowing Monks to use light armor while retaining their class features may feel like you’re losing too much of what makes a Monk a Monk, but it would mean they can actually expect an AC bonus.
Again, you can switch this around by simply providing things that offer “unarmored” AC. The important thing, however, is to not just offer AC bonuses, but also the special abilities that can be put on armor, and without the prohibitive extra costs associated with, e.g., rings of protection.
Ultimately, one of the biggest problems for the Monk is that he utterly depends on at least four different ability scores (Str, Dex, Con, and Wis), and it’s not like he wants to totally ignore Int. Reducing this will help.
Give him 6+Int skill points per level; that will put him on par with the Bard and Ranger, and allow him to be a little more in-tune with his “mindful warrior” archetype. Strongly consider abilities that allow him to base his attack and/or damage on Wisdom.
The other way to handle this, and this is perhaps more appropriate from the DM’s perspective, is to give him items that give Enhancement bonuses to all ability scores. No one appreciates that kind of all-around bonus like a Monk does. Again, the magic weapon that uses Unarmed Strike damage might also use Wisdom for attack rolls.
Giving Real Class Features
Shoring up the numbers (as discussed above) will help, but ultimately do not lead to a Monk that actually does things: the Monk has plenty of numerical problems but those are not his only problems. Giving the Monk mystical or pseudo-magical abilities is a great way to both make him special, and give him greater flexibility and versatility.
Perhaps they are the ancient teachings of his monastery, passed down in scroll form, written in a language taught only to their very best students. Or perhaps he has simply reached some level of nirvana. At any rate, some number of Divine spells, Psionic powers, or Sublime maneuvers are highly recommended. They fit the class and give it the actual abilities that it needs. These could be given in the form of special magic items the Monk finds, or require things like Stunning Strike uses, to make them unique to the Monk.
These problems cannot and should not be ignored
Other answers suggest that the problems don’t really exist, or that fixing them somehow makes the Monk not a Monk any longer: this is horribly untrue. I cannot strongly enough recommend that you look at your own game, see the problems that you, yourself, have encountered, and realize that these answers cannot be completely correct.
Duncan Matheson has a lot of really cool ideas for the Monk. However, most of them are things the Monk cannot really do, and none of them, even if you let the Monk do them, are going to allow the Monk to keep up. There are serious, mathematical problems with the Monk that must also be fixed.
The Monk is not as amazing at Acrobatics as implied. He has a high movement speed, but that doesn’t directly translate into anything except jumping higher/farther (and moving more per round, of course). In fact, with his low skills and heavy Multiple Ability Dependence that forces him to keep his Intelligence low, keeping all of the acrobatic skills (Athletics, Balance, Climb, Jump, Tumble, and so on) at high levels is very difficult for the Monk.
Adding in cross-class ranks to Use Magic Device is just adding insult to injury, in my opinion: Charisma is the only ability score that Monks can afford to really dump, and even hitting the DC 20 check for Wands is going to be difficult with cross-class ranks. Moreover, Wands are expensive, particularly with high Caster Levels that allow the Monk to cast them ahead of time.
Finally, as addressed in my answer about optimizing Monks, they are atrocious at Combat Maneuvers, which depend heavily on Strength, BAB, and size: none of which the Monks get.
Monks are supposed to be mobile, dynamic warriors, highly-trained and capable of exotic, even mystical techniques. Unfortunately, their actual class features are a mish-mash of poorly-thought-out, uncoordinated abilities that are weak, mutually exclusive, extremely limited, or, usually, some combination of these things. You need to give the Monk actual skills in order for him to feel like a skillful character. That means he needs special techniques that aren’t just worse versions of what the Barbarian or Fighter are doing. I recommend using spells, psionic powers, or the Tome of Battle sublime way for these things. These allow the Monk to be versatile and different from other characters.