Hi, many problems...
You need 10.4.11 or higher to be able to read the new drives with 4096 Byte Sectores of Adavanced Format, not sure if 10.3 can deal with NTFS either, If larger than 2.2 TB then PPC Macs cannot deal with it if it was Formatted APM Partition scheme.
Mac Compatible these days generally means newer Intel Macs only.
If your hard drive plugged into a Windows machine and worked, then it is probably formatted with FAT32 or ExFAT. For some reason, a lot of eMac's have trouble mounting disks formatted with such file systems. If possible, back up any data on the hard drive, format it to Mac OS Extended, and try it with the eMac again.
Also, it is trivial to try the ports with other devices that are known to work with the eMac, etc, etc.