I have to set up two different domains (and domain servers) on one LAN. Can I use completely different subnets? Would my unmanaged hubs have any issues with this? How about the main router? Any thoughts would be helpful.
There should be no problems with multiple subnets on the one LAN segment, with one exception, DHCP.
Because DHCP just broadcasts "give me an IP address" all DHCP servers on the LAN will get that request and reply. So if you had two separate DHCP servers you'll get PC's getting IP's assigned randomly from subnet A or subnet B. You can fix this by either:
a) Not using DHCP
b) Using static MAC to IP mapping and only using one DHCP server. That way when your DHCP server sees a DHCP request from aa:bb:cc:dd:ee:ff it'll know to give it an address of X.
Your router should have no problems at all, as long as it can handle having more than one IP address configured on it (on a Cisco this is called configuring a secondary IP address)
Your HUB will not care at all, it works at layer2 only.