My wife and I use a pretty simple system which we picked up from some friends of ours:
80% of each of our post-tax income goes into a shared account for stuff which is unambiguously 'shared' costs - for example rent, utilities, groceries, savings, stuff for our son, eating out together, etc.
We each keep 20% of our income to do what we want with. This fixes almost all feelings of inequality (I make a bit more than my wife. Personally I'm not that bothered, but my wife feels very strongly that she does not want to be 'supported' by my income, and that her disposable income should be based on her income, not our net income).
Every now and then we agree to move a cost into the 'shared' category even if it's clearly not a shared cost (e.g., my wife's phone bill comes out of the shared account because my phone bill is paid by my employer).
Sometimes we also 'treat' each other, by taking a cost like a dinner out together as a personal expense (often on pay day, for example).
As an exception to the above, my wife is on maternity leave at the moment so we agreed we'd just sum up all our incomings and each of us gets 10%. This is also working pretty well so we might not change it back after she starts working again, but we'll see if she raises this inequality thing again.
Obviously YMMV, but this system suits us well