I used timer events extensively in Klik & Reality, and I have yet to be eaten by a grue. Dunno what the fuss is about.

The problem with timer events is that they run on a separate timing system from everything else. An enemy that shoots bullets at timed intervals will be far more difficult, maybe even impossible, for users on slower systems. It also causes problems for MIDI (re)starts. Half the time I couldn't read the first string of text in each scene in snapman's "Dickens' Inferno" because it was set to cycle after just a couple seconds, which is almost as long as it takes to load the MIDI on my system (in Windows). The timing system behind timer events keeps going even while the MIDI is being prepared, which can create a number of unwelcome side-effects. These side-effects make themselves even more apparent in "the Dreaded Alt Bug" where you could press Alt in Vitalize! browser games to pause the game, with timer events still going, then press Alt again to resume the game and force the timer events to play a mad game of catch-up. Players could exploit this, for example, in games like Construction Bob, where the Alt Bug allowed the player to flood the conveyor belts with rocket parts in order to gain a ridiculous amount of points.

I wanted to leave the solutions as an exercise to the reader. And if I can make the list comprehensive enough, we get something where one small discovery will lead to the next, and the steps in between are done by applying previously learned skills with a little critical thinking.

As for how I did Choo Choo Text, open the .gam file and find out! Actually, what I did was use a waypoint system. It'll probably look strange from the code I used due to the workarounds I had to employ.