I think you'll need to increase it in the VM configuration in vSphere Client.
R-click on the VM, Go to 'Edit Settings'. On the Hardware Tab go to the virtual hard disk that doesn't have enough space and increase the provisioned size there. Of course, the VM needs to be off for this to take effect and, depending on the OS, you may need to go through extra steps to get the VM to recognize the extra space. For Windows server 2008 all you need to do is extend the drive in disk management.
For earlier Windows OS's you'll need to use 3rd party software after you have provisioned more space in vSphere. My favorite (and easiest, IMO) is G-parted. Boot the VM from the G-parted disk and in a few clicks you've extended the partition. If G-parted was successful, once you reboot into the OS it will automatically recognize the extra space.
I'm assuming that it's just the provisioned space for that particular VM that has run out. If you're ESXi datastore has run out of space that's an entirely different problem. If you have multiple datastores you could move the VM. If not, I think you can try and shrink the virtual disks for other VM's and give that space to the one running out. I don't have any experience in shrinking volumes using the VM Tools though. Maybe someone else can offer some more insight on that...