This really depends on your requirements (you haven't really given us enough to work on)
I would go for a single instance, especially if you are using linked servers in any way - at least you can just do cross database queries rather than using linked servers
multiple instances can help if your clients require a dedicated server, but it comes with the cost of having to manage the memory and cpu configuration very carefully. performance tuning can be a bit of an issue too... especially where each instance of SQL is fighting for disk resources.... you can't see in activity monitor why your disks are running slow without going through each instance.