Production network design idea: 7 sites total. Each site has an HP Procurve core switch. Each switch has at least 2-10G dark fiber connections to other sites. A few links are under 40km, the remaining are under 20kms. The legacy config was vlan tagging subnets on these dark fiber links, so multiple vlans and subnets spanned 2 or more sites over the dark fiber and many km. One main reason we did this was for VMware guest migration in a DR scenario. I now believe we need to redesign our dark fiber connections to be route only. Thoughts?
In short: whether you use L2 or L3 links doesn't matter in terms of distance or dark fiber. What matters is your network architecture.
Parameters to consider:
- size of sites
- administration of sites (central vs independent)
- site autonomy (DHCP, DNS, local servers)
- resilience requirements
While routed links are generally preferable, small sites that are administered centrally and aren't autonomous anyway might not really worth the trouble. L3 switches aren't expensive any more though - if any one or two of the parameters above make you think, go for the routed variant. Also, you can migrate VMs over a routed link just fine, it's just the bandwidth that is crucial.
 I'm assuming there's low latency - fiber itself eats ~49 µs/10 km one-way - and ample bandwidth in your network. Higher latency and bandwidth limitations demand routed links very quickly.