My second and third toes are fused together by some skin. I'd rather not have an operation to separate them as they are fun and unique, but they prevent me from wearing "five-finger" shoes.
To get away from toe injuries I've looked at Terra Plana's Evo shoes (http://www.terraplana.com/evo-p-1263.html?colour=271).
They look like something that might be the thing. But I have not so far actually tested them.
If you're going to run more trail-running or the like then perhaps a pair of huaraches might be something for you (http://barefootted.com/shop/).
For me they have been a mixed blessing. I tend to sweat a lot from the feet and thus the airiness of the sandals are really good for me. But it's been hard to learn how to properly string them on longer runs and small mistakes makes it easy for my feet to get blisters.
(I'm co-owner of CrossFit Quantum and we teach forefoot/POSE running as part of our movements.)