I own a few multi-units (duplexs, tri-plex and one 4-plex) and have this dilemna with some of them. A few have all utilities completely separated, but some have only one water line. In these instances, I pay water and sewer for the building. In my experience, the water/sewer expense has not been overwhelming and I slightly increase the rent to account for it.
I have looked into running separate water lines at several of the properties but I could not really justify the expense. In one property, it would cost about $2600 to add the additional line (cost of the line plus the city "hook up" fee). When my average water/sewer bill is running me about $33 per property, it is tough to sink the money into the new line.
In general, the monthly water/sewer bills on all of the properties are fairly predictable so I have built them into what I ask for rent.
That said, I have avoided properties in which the gas or electric utilities are not separated because I could see those bills getting out of hand quickly and fluctuating wildly from month to month (and tenant to tenant). I have absolutely nothing to base this on as I've never owned a property like this, so it is just a built-in bias. I would be interested in other owners' thoughts on single gas/electric metered multi-units.