Is it bad to stack your equipment

Bgrazman is right. Stacking can negate the very purpose of clean/dirty boxes. Also consider that the likely hood of scratching componenets or leaving traces of rubber footings increases dramaticly. This can devalue your equipment for resale. Those racks serve a purpose.

If you invest significant dollars in components because you think it's a good thing if one wants great sound, how on earth could you, or anyone, contemplate stacking them like pancakes? Do the right thing ... buy or make your own rack to hold equipment that either cost significant dollars or that you value for their performance. Too, a good rack adds to the overall listening/aesthetic pleasure. These things really do matter, don't you think? In my case, the Sanus Euro-rack works/looks just fine! Not that expensive, actually, and easily adjustable to meet changing needs. Go for it!

There are many issues in play, but yes, it is bad to stack. Some pieces of gear are very sensetive to electrical fields, and some pieces of gear throw out a big electrical field.

Amplifiers can interfere with CDPs and pre-amps. Racks can be made cheaply (you get what you pay for though) but better racks (read: more expensive) do a better job of stabilizing and islolating/coupling gear.

Some people go to great lengths and costs to seperate gear, and the results are worth the effort IMO.

If you're able to do easy woodwork consider building a diy Salamander clone rack. They easy to build if you're handy at all. The beauty though is that you can design it anyway you need and the shelves are always adjustable as equipment changes. Also they're very strong.

What Nrchy said above is a good reason to avoid stacking. Also the better you can get rid of the heat the more reliable your electronics will be assuming you keep them for years which many of us don't.