I really recommend ProEXR. http://www.fnordware.com/ProEXR/
You can write out a single EXR with all the layers in different channels or you can export all the layers as separate EXRs. The EXR maintains metadata so if you are python savvy you can write something that will auto comp it for you with the correct merge modes and opacity setting. The last time I talked to him was was really close to having a nuke tool that will do just that. Quick tip: When you write the EXR image from PhotoShop using ProEXR, it defaults to PIZ compression but Nuke is really slow at reading those. I've had much better experience with RLE compression. If disk space in no object NONE compression is even faster in Nuke.
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