How does one ditch a bad boss (resign) without having it count against you in future job applications?

Just don't put them as a reference. Get someone else at that place of employment to be a reference for you, or make sure you have enough references from previous jobs.

First, swallow any desire for revenge or payback in the process; burning your bridges is the single largest mistake most make when leaving a position. There is no benefit to it other than a momentary satisfaction, but the negatives will stick with you for a long time. So resist those urges.

It is easy to just submit a letter of resignation that is short and succinct. You don't even have to specify any reasons in the letter. When talking to the boss about it, it is perfectly reasonable to say that you have a personality conflict or whatever it is that is getting in the way of you being able to contribute 100% to the company's goals and you would rather seek other opportunities instead of prolonging this and it getting worse over time. Be reasonable and calm, even if he/she/they are not, let them rant and "dis" you without responding in kind. They will later remember how you comported yourself if/when they are called for a reference.

There is never any need for this process to be dramatic; don't make it so.

Depends you can always say you wanted to improve your position if yuo make a move up the ladder. If at Micky D's it matters little.

Beware unless YOU are the BOSS you will never full like a boss so be sure it is worth leaving a good position over.