My awesome, handsome, and spectacular husband (who is typing this) and I are traveling from Lübbenau, Germany to Münich by way of Prague. I know the Czech Republic does not have checkpoints for stamping passports, but we would like to have ours stamped as a memento. Where can we have this done?

You can't. I'd love to have a stamp from Vienna too, but looks like I'll only be stamped by Roissy on the way in and Schiphol on the way out, if at all.

The old Praha passport stamp (before EU) was one of my favorites.

we flew from London to prague and that way our passports were stamped-so at the airport but not sure if you are flying.

As you are crossing internal Schengen borders, there is no routine passport check and no stamp, whether you travel by air, road or by train. There are occasional spot checks on international trains - but officials don't stamp passports, and are on the lookout for illegals, contrabands etc, so often only certain passengers are asked for their passports/IDs or to open their luggage.
There is really nowhere you can get an immigration stamp coming from Germany. A country like Liechtenstein (not yet in Schengen but has no passport checks by its officials coming from either Austria or Switzerland - Swiss officials man the border with Austria; no airport with non-Schengen flights) offers to stamp your passport as a souvenir at their tourist office, for a fee. I wouldn't want to mess up an official travel document with souvenir stamps, frankly.