After everything is all-said-and-done, what should I use to clean up my flasks? Can tubing be used from one reaction to the next, or should it be cleaned or even disposed of? If you think of anything else to add, feel free.

you dont need to dispose of anything unless it won't get clean. to clean i just use water under pressure ir even just water. there are also cleaning fluids for some reactions.

It depends on the nature of the leftovers in the flask, if organic I use a little petroleum ether to remove stuff then wash with detergent and water, rinse with dH2O then rinse again with acetone. The acetone can be omited but it makes for sparkly dry glasware. For stuborn organic deposits you can use toluene or DCM as they may work better. But over all for the worst crud or if you are just lazy make up a really strong NaOH or KOH solution and pout it into the flask taking care not to get it on the joint. This will eat some (very little) of the glass away and any deposit you could get on your glass, and the glass will be ultimately clean, there is not stronger glass cleaner available. Rinse with bicarbonate and water and water then acetone as usual. You can also use HCl to clean glass but I 've found it to be too weak for pretty much everything.

Silicone grease is notoriously hard to remove, I forget what removes it(NaOH?) but I'd just prefer to stay away from it. FYI: If you heat silicone grease on your glass in an oven it will destroy the glass by crystallizing it.

i have found that Denatured Alcohol is the best. followed by a good rinse of d-h20.

I've always been able to get away with DCM boils, followed by good ol soap and water wash. Shit like isomerization crud is a bitch to get out. I usually get away a few times, and end up throwing the flask away. But no more since SWIM switched to microwave isomerization.

This is off topic but mad: do you have a microwave reflux setup? hole in the top of you microwave? or some other setup? do you use vacuum with that?

Maybe. SWIM has been to the Thrift Shop and picked up a cheap ass old one (the type with the dial timer, that dings when done, like a little oven timer or something). No vacuum needed.

My baker likes the yield he gets with a vacuum cleaner.

stong acids or basic solutions clean glass well. also go to home brewing stores they have a wealth of glass cleaning stuff. i forgot the name of it but they sell a fitting that attaches to the end of the spout that shots a strong stream af water for those hard to reach places.