Medics can crack the backbone of the enemy assault just as easily as they can run flags.

Dirty Tactics
   Remember, you are protecting your base from the enemy.  Suppose you run into an enemy that is the same class as you.  Exchange shots, and by all means try to kill him.  But as soon as you have done some substantial damage to him (and/or taken damage yourself) you should run back to your resupply.  Restock, and then run back out to engage the same enemy.  You should kill him, even if the enemy lands more shots than you do.  Fair?  Not really, but you have to take advantage of the fact that you are on the defense, not him. Learn this tatic, it seems simple and everyone brushes it off as a basic tip, but i rarely see the tatic performed on public servers, or any servers for that matter.  Learning to so this will enable you to hold off much more skilled players than you- just because you know how to play D.

Intercept secondary routes
When you are standing inside your base, right under the 2FORT sniper nest, you will often enemy see spys and scouts jumping into the water.  When you see this, hurry to the top of the spiral staircase.  This is an excellent spot to hold for D.  As you hear them coming up, get out your shotie, and then toss a grenade down the steps.  the spiral will carry the grenade quite a long way down, which catches the enemy off-guard 90% of the time.  Once the 'nade hits him, go down there yourself and finish him off with your gats. 
  2FORT isn't the only level for this.  On WELL, it is very common to see enemys take the route with the blown grate in the front straight to the flag.  As a medic, you dont ahve to kill the enemy to be effective. Suppose you see the enemy swim into the tunnel.  Hurry to your flag room, and hide in the water under the bridge. (the bridge by your cap point) .  When the enemy comes by, swim out of your hiding place and infect him.  This is especially effective when dealing with the Soldier and HW classes, since they are so dangerous one on one.  After you infect them, just run away (lab a grenade if u must, but dont fight).  Byt he time they get the flag, they will be weak and dying.
Protecting the Flag
This is one of the most difficult things to do in TFC.  Killing the person with the flag isn't all that hard, but after you kill the first bum rusher, you know that more ensue.  Adding to the difficulty is that bum rushers often employ a very useful tactic, known to many a player round the world as "spam".  This means chucking grenades and firing rockets at reckless abandon.  When protecting the flag, also know that killing the enemy after the flag is touched is no good:  The flag return time is reset at 60 seconds.  
So what can you possibly do to prevent a flag cap?  Well, fpr starters, you need at least one other teammate to help you defend.  If you see a spy or scout nearby, try to get them to lay all of their caltrops/gas grenades.  Lastly, you need at least a couple of your grenades in your disposal.  Pump up your defending teammate all the way (max health) and prepare for a battle.  Get ready to duck for cover from grenades, and to heal up your teammate every ten seconds or so.     

Knock out Spys
Spys have to be the biggest headache for an opposing defense.  They take out your sentry guns, turn unsuspecting HW guys into easy gibs, and leave teammates fighting for health packs in the respawn due to GAS grenades.  Well, all of the above gives a pretty clear explanation why you, as a medic, must take out enemy spys when on defense.  When dealing with spys, one must use his/her brains first, then gats. 
1. Spys must have the default weapon out
If you see an engy with a shotgun, dont shoot him.  If he were a spy, he would have a pistol out, and it would not change, even if he switched weapons.  You will save yourself some ammo and getting      yelled at if you pay attention to what        weapon a player has out.
2. Feigning spys have weapons
Feigning is a popular tactic among spys. They will knife sommebody, run away to a shady place, and play dead in a corner.  When you are looking for a feigning spy, you dont have to press your medkit to every single dead body.  If the dead body really is a spy, they will have their weapon out.  Sometimes a pistol; sometimes a kinfe, but they will alwasy have some sort of weapon out.  Also, keep in mind that a feigning spy takes up space on the ground.  You might be walking up a ramp and all the sudden you are stuck.  This isn't a bug, this is most likely a spy playing dead. Crouch, and use your medkit on him. 
    Lastly, keep your ears tuned for the sound of a player dying.  Often times (especially in low-traffic areas like the 2FORT basement) you will hear a dying noise, yet no one was killed.  If this happens, head straight for your flag and check for all dead bodies near it.
Be on the Move
As a medic, one of your most precious advantages is your speed, second only to the scout.   On maps like WEL and ROCK2, your defense is spread out.  The bulk is probably concentrated in the yard, you will have some sentrys at the front entrance, maybe some HW guys covering the Key entrance, and at least a sentry or two centered in the gas room or near it.  A A spread out defense helps contain all areas, but suppose the enemy broke through the yard and has the key.  When you yell "Seal off the Gas chamber entrance!"  do you really think that those slow ass soldiers and HW's at the front entrance are going to make it on time?  HELL no!  Its your job to run to the yard.  From here, stay close to the gas entrance.  When you see the flag carrier, DO NOT just run up to him and throw grenades (except maybe medic or sniper) .  Just hold your ground, and let him come to you.  You will have to do some dodging, especially if the key carrier is a soldier.  You probably wonder why I would tell you to hold your ground and get shot at and not attack.  Answer:  Medics are  untouchables to every other class.  When an enemy sees a medic, they either run away, or try desperatly to kill him, just out of fear of being infected.  By holding your ground, you can make the enemy worry about killing you, and in the process buying time for your teammates to get there.  Even if you die, the time the enmey wasted is very helpful.  now, it is up to your team to kill the carrier.  Now do you see why the presence of a medic is dangerous, even if you aren't shooting anything? 
House calls
Remeber, you are a medic.  Medics can kill, but first and foremost they heal.  Keep your eyes pealed for teammate messeges that say they need healing.  In most maps you can scurry back to your base fairly quick.  Other times, you will play in bigger maps and you need to get something done.  When this is the case, cue a string of messeges that say "Ill be there soon,  Stay in the back respawn and Ill get you ASAP." Now, some people would say this is a questionable tactic.  I'll know that it is risky, but if you are true to your word, the respawn medkits will keep them alive long enough for you to get there.  It also helps to have certain binds on your keyboard.  I have these two:
1.  Where are you? (when they say they are infected)
2.  Just wait, I'll be there in a little bit (in terms of I'll meet you somewhere soon where I can heal you)