Are side effects a good thing?

Side effects are a necessary evil, and one should seek to minimize/localize them.

Other comments on the thread say effect-free programming is sometimes not as intuitive, but I think that what people consider "intuitive" is largely a result of their prior experience, and most people's experience has a heavy imperative bias. Mainstream tools are becoming more and more functional each day, because people are discovering that effect-free programming leads to fewer bugs (though admittedly sometimes a new/different class of bugs) due to less possibility of separate components interacting via effects.

Almost no one has mentioned performance, and effect-free programming usually has worse performance than effectful, since computers are von-Neumann machines that are designed to work well with effects (rather than being designed to work well with lambdas). Now that we're in the midst of the multi-core revolution, this may change the game as people discover they need to take advantage of cores to gain perf, and whereas parallelization sometimes takes a rocket-scientist to get right effect-fully, it can be easy to get right when you're effect-free.

Every so often I see a question on SO which forces me to spend half an hour editing a really bad Wikipedia article. The article is now only moderately bad. In the part that bears on your question, I wrote as follows:

In computer science, a function or expression is said to have a side effect if, in addition to producing a value, it also modifies some state or has an observable interaction with calling functions or the outside world. For example, a function might modify a global or a static variable, modify one of its arguments, raise an exception, write data to a display or file, read data, call other side-effecting functions, or launch missiles. In the presence of side effects, a program's behavior depends on past history; that is, the order of evaluation matters. Because understanding an effectful program requires thinking about all possible histories, side effects often make a program harder to understand.

Side effects are essential to enable a program to interact with the outside world (people, filesystems, other computers on networks). But the degree to which side effects are used depends on the programming paradigm. Imperative programming is known for uncontrolled, promiscuous use of side effects. In functional programming, side effects are rarely used. Functional languages such as Standard ML and Scheme do not restrict side effects, but it is customary for programmers to avoid them. The functional language Haskell restricts side effects with a static type system; only a function that produces a result of IO type can have side effects.

In von-Neumann machines, side effects are things that make the machine work. Essentially, no matter how you write your program, it'll need to do side-effects to work (at a low level view).

Programming without side effects means abstracting side effects away so that you could think about the problem in general -without worrying about the current state of the machine- and reduce dependencies across different modules of a program (be it procedures, classes or whatever else). By doing so, you'll make your program more reusable (as modules do not depend on a particular state to work).

So yes, side-effect free programs are a good thing but side-effects are just inevitable at some level (so they cannot be considered as "bad").