"In cases when" vs. "in cases where"

I would say "in which user's needs...". You are referring neither to spatial nor temporal location.

Go with 'where' because, as @Alenanno states, you have said 'in cases' which hints at a location, though an abstract one.

You could use 'when' with a slight reword: '...suitable at times when...'.

@Mickeyf 's suggestion (in which) would normally be a good substitute but in this particular case it would leave you with a repetition of 'in', which sounds clumsy. This option would fit better if you went with '...suitable for cases in which...'.

So, I would say that those are your choices.

Hope that helps.

The sentence seems to me to be excessively wordy. The tendency to embellish sentences, in the hope of adding an air of authority, should be resisted.

Methodology X is more suitable in cases where users' needs are well understood up front.

Why not simply say

Methodology X is more suitable if users' needs are well understood.

Though the context ought also to tell us the specific methodology with which X is being compared.

From Gartner's modern usage guide, I gather avoid using cases altogether.

For example:

Methodology X is more suitable in cases where if users' needs are well understood up front.