Now, the hard drive does not seem usable after waking from sleep - I can hear it spin up, but I am left with the spinning beachball of death, and keyboard/mouse do not respond.

I have left it like this for hours, and control never returns, computer must be forcibly turned off using the power button.

Is the clock battery in good order? Did you trip the PMU reset button after re-installing the drive? I usually reset this whenever making hardware changes.

Don't know if it will help, but here are a few tips that might get you out of the situation.

Good luck.

the hard drive does not seem usable after waking from sleep

Just from this line and with no technical knowledge, it sounds like a power management issue. Reset the PMU, like suggested.
Unfotunately I don't know where it is on an eMac.

it sounds like bad ram. I had the same thing happen to me with my powermac g4 mdd and my imac g4. The internal ram was failing and every once in a while I would get kernel panics. The system goes to sleep and then does not wakeup and then theres the problem your having which was the same as my imac g4. I replaced the internal ram and it was fine after that. Its not your clock battery or any other bull crap I guarantee its your ram

I don't think anyone suggested it was the clock battery.

Mmm, cost to reset PMU first: nil

Cost to replace all the RAM with new RAM: more than the value of the eMac you'd be left with. ie. you could spend £80 replacing the RAM and be left with an eMac worth £40.

Used to happen on the MDD because of the PMU too, it had to also control power to an ADC connected monitor and maybe Apple Pro Speakers.

I never said that was not the cause all I said was I had the same problem and it was ram. I never said don't try the above method of pressing the pmu button on the motherboard and all I said is I had the exact same problem and the solution was replacing the ram.

And I would have agreed with you, but the original poster made no mention of experiencing KP's during normal operation. I've had RAM go bad on my MDD as well, but it always showed up as a freeze or KP, or nothing at all (if the RAM was not in use). When nothing happened, I could open ASP and see that slot 3's 513MB stick would report as 256MB, then 5 minutes later, Empty. Restart and it would show as 512MB again, for a few minutes at least. Of course I only had top spec Apple-approved RAM (from an Apple Premium Reseller) and it came with a lifetime guarantee.
Funny really, walked into the shop some 4 years after buying the RAM, with the original receipt, said "I've got cooked RAM", he said "Not a problem, here's a replacement, sorry about that sir".
And like you, my MDD was a pain to wake from sleep sometimes. I'd reset the PMU and all would be fine for 6 months or so. If I switched to the DVI port (ADC monitor through an Apple ADC-DVI adaptor) everythingwould be fine all the time. Seems having the PMU controlling power to 4 HDDs, 2 optical drives, Apple Pro Speakers, KB and radio mouse AND the Studio Display was just too much after some 400-500 sleeps.

But of course, the OP's Mac is an eMac, and there are no KP's - the screen wakes, the HD spins up and he/she gets a freeze.
Could always look in the Console logs, cost: nil, but I doubt there's anything usable in there - but look anyway.
Could always repair Disk Permissions, cost: nil.
Could always Verify / Repair Disk in Disk Utility, cost: nil.

what would happen with mine would It would work normally but after a little while of use it would kernel panic and then I would reboot and again it would kernel panic after about 20 minutes of use. I also could not put it to sleep. When I put it to sleep it would not wake up. The fans would roar back up but the system screen would stay blank. I replaced the ram and it fixed everything. No more kernel panics and the system went to sleep perfectly fine. Sorry I did not mean to say to replace the battery I meant he probably did not have to press the pmu button on the motherboard referring that is problem had to do with ram. Sorry for confusion :]

Maybe I spoke too soon, and you could be spot on.

OSX 10.4 is very fussy about RAM quality, and OSX 10.5 is even more so. Rather than cooked RAM, it could just be slightly too slow, or underpowered (PMU again). Perhaps the OP should check the RAM specs in ASP to make sure they're reported as they expect. I've seen PC133 branded RAM reported as PC100 when it's been marginal in OSX 10.4. It's a good sign to replace it.

exactly same thing that was happening to me in 10.5.5 on my G4 MDD the ram was pc 133 and in system profiler it was reported to be pc100 which clearly it wasn't and the clock speeds of the ram where also wrong. I replaced the ram with new stick of pc133 and everything showed up fine in system profiler including clock speeds.

Close, it'll be something like that. The MDD takes DDR RAM, PC2600 or PC2700 or PC3200. Maybe they were being reported as PC2100.