TL;DR:
- Design encounters with what your players and PCs are capable of doing in mind but do not blatantly block their hard earned abilities.
- Disallow/change beforehand what you think can be harmful to the game.
- If something slips through the cracks, talk to that player and make necessary changes.
- Always have backup complications (use Damage, Disruption and Duration).
I’ll chime in with what I do.
First, the issue with “problem spells”… These exist in any game system probably. ICRPG is worse in this regard. Between ICRPG MAGIC and Khan’s SPELLS & FEATS, there are many powerful SPELLS, some of them even potentially game breaking.
Yet, the spells themselves aren’t the problem, but designing modules without taking these into consideration is. Actually, this is a lie too because this is not a problem either because this is not feasible.
The real problem is designing rigid modules/adventures with predetermined steps and endings. In such a case, modules can be trivialized with having the right spell/ability or using a spell or abiliity in a creative way.
In the thread you took my quote from, I explicitly mentioned that every adventure (especially published ones) needs lots of backup complications and situations in case something goes wrong, as in something is broken by players due to lucky dice or clever/out of the box thinking. Like @KaneDriscol said, using 3Ds and using them mercilessly solves most of the problems because players won’t have enough breathing room to “break” any planned encounter.
For prepping one’s own game night, everything is way easier because you know all players and all PCs and what they are capable of. You can and should design around them (without making their hard earned skills/spells worthless). They will still surprise you and break your encounters in ways you could not have foreseen but with each passing session this will be rarer and rarer.
Kelsey’s work in preparing the list of problem spells is great but unncessary in the hands of a skilled DM. I’ll spend my time creating complications rather than thinking about how players might break my encounters. Actually letting them break a couple of encounters makes them feel great, so there is nothing to worry about.
Also remember that just because something is written in some book doesn’t mean you have to use it. I always write in my books that you can disallow/change/remove anything and everything you don’t agree with. If you couldn’t anticipate that a certain character ability would cause you problems but you only see it in game after a character earned it, talk to the player and replace that ability with something else.
Table health is important.
