You can let Spybot remove entries for several undesirable programms and applications at once. It don't increase the risks and can realy save you lot of time. Anyway, Spybot will ask you if you want to make a backup before any changes are done. It's a mostly un-needed safety mesure.
Nothing BUT the entries for those pests will be affected.
Most spyrares and other crapwares do indeed polute the registry with many redundent entries. It's done to make it harder to remove them. But it's not because there are LOT of registry content to purge that it become unsafe.
You don't need to wory, Spybot is a safe and reliable application.
The warning about not doing to much registry changes at once is only about doing those changes manualy.
In that case, you do ONLY ONE manual change, check if everything works as expected, then proceede to the next manual change.
When done by an installer/uninstaller, virus scan and repair, spyware scan and repair and some others, you can easily have over 100 changes done at once, if not more.
Electro, August 2012