A customer has 3 sites, and wants a single /24 over all three. All are geographically separate, and no p2p links between them exist. Plenty of bandwidth at each location. I was going to use IPsec and EOIP, unless someone can give me a reason this wouldn't work, or a better solution? Are there any advantages to using L2TP?

Depends on how much security that you want. IPSec is going to get you more encryption and security, but lower throughput unless you get a RouterBoard with the IPSec accelerator at each end 1100AHx2 is currently the only model with that if I remember correctly. What you are talking about doing is basically an adaptation to this, just using the internet instead of wireless links, and setting up an IPSec policy over those EoIP links.
http://wiki.mikrotik.com/wiki/Transpare ... %28EoIP%29
I have also had problems at times building an EoIP tunnel across the internet to some sites, though every other tunnel works fine, so I wrote it up to the ISP doing something weird that prevented it.

If encryption is not as big of a deal, a PPTP or L2TP with EoIP running on top of one of those PPP interfaces will work fine as well, and probably be easier to setup and get going.

You do not need EIOP I think.

PPTP link (should always work), Briding enabled on both sides (obviously on both sides), then you can use the bridge interface.

No need to run EOIP on top.