Fergus, I would lean towards option 1 as well. However, there is the a mid point you can use to save costs. I have worked in a datacenter where they put a telco rack with switches at the beginning of every row and then ran network cabling in to the racks from that telco rack. If done right and managed properly, you can pull this off nicely. This would allow you to save costs on patch panels as you will be running large patch cables to these racks. I myself personally like having patch panels running directly to each cabinet and then heading back to a central patch panel area within the datacenter.
I would double check the fiber sizing that you mentioned with the 50micron fiber. I have seen equipment use 62.5micron more and more these days. I do not recall ever having to go down to 50micron fiber. By using 62.5micron fiber, you can also get more diverse in the fact that you will be able to use with servers and network gear in addiction to the FC.
There are many different ways that you can configure the cabling. It all depends on your environment and the size of your environment as well as your budget.
Additionally, Have you considered using cat6 as opposed to cat5e? It is a little more costly but is specifically optimized for GigE.
Good luck. I think you are on the right track!
--Keith
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