BJC-6000.WASTE INK TANK.

What Canon calls the "waste ink tank" is really several very thick felt pads stacked on each other. Cleaning cycles pump ink out of the heads and a hose sprays it in a pad so it soaks into the felt pads from the bottom up. The printer simply counts the number of cleaning cycles it has performed and when it hits a certain count it warns you, when it hits a higher count it stops printing. Good news, bad news: you can reset the printer, but if you don't replace or clean the waste ink pad you run the risk of overflow.
This is straight from the CANON Australia service manual.
Follow the steps carefully to reset the Waste Ink Pad Full condition.

1. With the printer powered off, press and hold the RESUME button, press and hold the POWER button. The buzzer will sound once.
2. While holding down the POWER button, release the RESUME button. Press the RESUME button twice in succession, and then release the POWER button. (Each time the RESUME button is pushed, the buzzer will sound once.) The indicator will blink in green, and then light in green.
3. Press the RESUME button 3 times.
4. Press the POWER button. The buzzer will sound once. The printer will switch off itself after performing the function.

Note that when I say left and right, I mean -your- left and right, not the printer's left and right.
After you have done this and confirmed that it is reset and printing again, it's time to remove and clean the waste ink pad, and the rest of the printer as long as you have it open. Following are instructions based on the BJC-6000. Most Canon printer cases seem to be built along the same lines.
First, get the cover off. You'll need to remove the parallel port cover first. There's a slot at the bottom of the parallel port cover, stick a flatbladed screwdriver in there and gently pry it out. Most Canon printers are very similar.
There are 4 Lights! Er, there are 4 plastic tabs holding the top on. You can reach the front ones by reaching inside the printer and gently bending them back while lifting the top.
The other two are on the sides near the back. There are slots, press a flat bladed screwdriver gently in the slot to push the tab back while gently lifting the top. DO NOT PRY!
All the Canons I've taken apart then have four screws that hold the entire printer mechanism on the plastic base. Some models do have a power supply module that slides out of the rear of the case, remove this first. -Only- remove the four screws holding the printer mechanism onto the lower case. Some models may have more screws, but becareful not to remove any other screws! It just lifts off. Set it up on a couple of boxes or chunks of wood under the tabs so the mechanism is reasonably level.
Now is a good time to take it outside and use dry canned air to blow out the paper dust in the back of the printer. Do -not-, repeat NOT use an air compressor! It is too much pressure, and air from a compressor or air tank is full of moisture and oil. And stay away, AWAY from the print head and the park pad and cleaning pump under it. Stay away from the paper path under the print head groove. If you don't, you can end up blowing ink sludge around the printer or blow air into the heads or inadvertently create a suction that pulls ink out the heads and blows it around the printer.
If you aren't wearing rubber gloves by this point, put them on now. The waste ink pad can hold an -incredible- amount of ink, partially dried so it is a lot more color than it looks. Do -not- do this in your bathroom sink! If your porcelain is worn at all or has any invisible mineral deposits, the ink can permanently stain it. Open a couple of windows and set up a fan as you'll be working with ammonia and alcohol. I know from experience that the fumes can sneak up on you.
Mix up a liter of cleaning solution in a clearly labeled, resealable container:

• 1 part nonsudsing household ammonia (clear, no perfumes)
• 4 parts 50% Isopropyl Alcohol (aka Isopropanol) (clear, no perfumes)
• 5 parts filtered or distilled water (-not- purified)

Take the waste ink pads out and lay them down on some newspapers by the sink. Chances are, it is no more than 50% color, as the waste ink warning is conservative so you don't end up with ink running out on your table.
Take the bottom printer case and run hot water over it to wash the ink out. You don't need to get it like new, just get the big blobs of goopy ink out. Pour some of the cleaning mixture in to help break it up. Dry it out with an old towel or paper towels and set it aside to dry.
Set the waste ink pads in the sink. Pour some of the cleaning mixture into them to dissolve the ink, then gently run hot water through to rinse it out. It will never look clean, don't try, just get it so there is little ink left in the wash water. It is a rather fragile felt-like substance so if you try too hard, you can end up destroying it.
Squeeze out as much water as you can. Do -not- twist it like a towel! You'll have to let it dry for several days. Put it over a heat vent if you have central air heating, or just in a sunny window. If you don't put it somewhere warm or with some air flowing, it will stay damp a long, long time. You can even lean it up against a box fan on low. I caution -against- putting it in front of an electric heat fan because of the fire hazard.
I have considered running a tube out from the park pad's waste tube to a bottle outside the printer. However, if you do this you run the risk of the bottle getting knocked over or leaking.
Look over the printer mechanism. You'll see some areas of ink build-up. Ink and paper dust mix to make a viscous mud that stays wet for a long time. I use cotton ear buds (aka Q-Tips or cotton swabs) to pick up the blobs, it is better if you can get some of the absorbant foam swabs. Then a premoistened window wipe to wipe off the rest.
Note: Don't use paper towels! Paper towels are horrible things that shed little bits all over. Any little bits that get on the bottom of the head, or on the park pad will cause ink to wick out or block a nozzle. Test the premoistened window wipes you intend on using; tear one in half. If it looks a bit like you tore a sheet of paper it's good; ie, a ragged but basically clean tear. If it looks like a cotton ball exploded it's bad! IE, threads or filaments everywhere.
I use Coralite brand window wipes. Ironically, cheap is better. No lemony scents, no vinegar wipes. Just plain old ammonia based premoistened window wipes.
After everything is dry, reassemble everything but the top of the case. Locate the lid detector switch, it is usually somewhere near the hinge of the lid. Use something like a small piece of vinyl electrical tape to hold it down so the printer thinks the lid is shut. After confirming that everything is back in place (except the top case), plug it in. Turn the printer on, confirm that everything moves as it should on power-up (basically nothing sticks or bangs).
Take the tape off the switch so it thinks the lid is open, this should cause it to move the print heads to the Cartridge Change position. Unplug the printer! This is important, so it doesn't suddenly decide you are taking too long and move the heads. If you have a holder for the print heads, take them out and put it in it. If not, set the print heads on top of a folded up premoistened window wipe. Ink will wick out, so you don't want to leave it too long this way.
Using several of your lint-free premoistened window wipes, carefully wipe up around the park pads. Careful! The park pads "float" in their holder and if you are not gentle you will knock it out of it's mount and it won't seal to the print heads properly. You may use a cotton swab moistened with cleaning solution to get the clumps, but don't touch the foam inside the park pad with it. That foam is really a hard plastic and will grab bits of cotton fiber and cause ink wicking.
Use an eyedropper to put cleaning solution into the park pad foam until it is visibly wet and wick it back out with a window wipe. Repeat. Again, you aren't going for spic-and-span, just the bulk of the ink. Put a few drops back in so it just looks wet.
There is a rubber and felt wiper just to the left of the park pads. It is probably retracted (towards you) but don't try and force it out. If it slides out easily, fine, again get the blobs off with dry swabs. Then wet the swabs with cleaning solution to get most of the ink off, and to get some of the ink out of the felt that is on one side of the wiper blade. Be gentle! It is very easy to accidentally knock this off of its mount or pull it out all together.
Without flipping the print heads upside down, wipe off the excess blobby ink around the edges. It is imperative that you do not touch the heads anywhere with cotton swabs, cotton cloth, or paper towels! Use the lint-free premoistened window wipes, and do -not- press against the bottom of the heads at all. I fold up a window wipe into sort of a cushion and wipe gently across the bottom. Do this only after cleaning around the edges or you'll just wipe that ink/paper sludge across the print nozzles. Again, it does not have to be spotless.
Reinstall the print heads, put the tape back on the lid switch. Plug the printer in, turn it on, let it finish it's cleaning cycles and gyrations. Turn the printer off again.
On my BJC-6000 and several models, you can get it to print a nozzle check by holding down the Resume/Paper Feed button while turning it on. It beeps once when you turn it on, let go of the Power button but keep holding the Resume button. If you let go after one beep, it does a quick head clean, if you let go after two beeps it prints a nozzle check and alignment check. Three and it just feeds a sheet of paper. Or just connect it to your computer and use the driver Maintenance menu.
Confirm everything is printing correctly again, power off and reinstall the top case. Your Canon should now work for many more years.
If the printheads are badly clogged and the printer driver cleaning cycles aren't fixing it, you may try the following:
First effort: put a few drops of cleaning solution onto the park pad "sponge". This is that sponge-looking thing (actually a hard plastic foam) where the head sits when not printing. Just do whatever it takes on that printer to unpark the heads as if you were going to change cartridges, then close it up and let it sit for a day before you run a cleaning cycle and nozzle check again.
Extremely Thorough Cleaning: Take the head out, remove the cartridges. If you've saved the orange seals, tape them onto the cartridges, if not then wrap black electrical tape around so it covers the ink outlet and the little air inlet on top. Only pull it snug across the ink outlet, not tight, and fairly loose on the cartridge body to prevent tape creep.
I then just stick the head under a stream of hot tap water. I use a soft plastic eyedropper to squirt the above cleaning fluid into the ink inlet meshes on the head and to flush ink off the bottom of the head. Careful not to touch the nozzles!
As you squirt cleaning fluid into the screen, a lot will rush back out, that is fine as it is flushing ink and gunk back out rather than forcing it through the nozzles, which are far finer than a human hair.
When you see little or no more color in the water or cleaning solution, force some of the straight filtered/distilled water into the screens. Rinse the outside of the print head with straight isopropyl alcohol (99% is better than 50% for this) and pat dry with a clean cotton towel (-not- paper towels) and again, DO NOT TOUCH THE NOZZLES.
Patience is a virtue. I've bought a lot of Canon printers in thrift stores with full cartridges because the heads clogged, they bought new cartridges, that didn't fix it so they tossed it at Goodwill. I clean them up and for $12.95 I get $45 worth of brand new cartridges and a backup printer. I only had two heads be unsaveable, those would print on all nozzles but had sprung internal leaks between two colors, cyan and yellow. The symptom was yellow nozzle checks print green, and the ink inside the yellow cartridge slowly turns green.