Fiber connections are very easy to use and offer the advantages of never being out of style. Who remembers trying to upgrade the copper cable plant from CAT3 to CAT5 only to see CAT5E show up? Fiber is fiber for the most part unless you plan to extend your demarc or IDF out about 2-3 kilometers. Then it gets fun.
Anyways.. multimode is cheap, 62.5 is the normal size you want (But Netapps want to see 50micron but work with 62.5). You want to see two PAIRs pulled in, one lit up and one dark but terminated for failover. Or have both lit up if you have the ports and let spanning tree sort it out or use channeling to pair them together. Once you have fiber in place, you really do not need to worry about your main data runs again in the long term future.
Cisco uses two styles of GBICs for fiber, an older larger BIC and a newer one called SFP which is much smaller and uses a different connector. Always have a couple of spares as they do burn out. But there are "Cisco" branded GBICs coming out of Asia on eBay that are very cheap so you really can afford the spares. I put Cisco in quotes because even when I look at them very closely, I can not tell if they are real or not but they work.
With respect to the switch fabric load on a 3500 series switch, they have very high speeds. I run over 70 servers and two Netapps with 8Tbs on them and 4 64Bit SQL boxes hammering away on 4 3560s chained together plus the users. Not ideal by any means but the switches are not the bottleneck and the stats prove it. You would be hardpressed to pass that much data to overwhelm the switching fabric.
The break even point a few years ago for the chassis solution vs the stackables was 350-400 ports. That probably has changed some as the prices of the stackables has really fallen alot in the past two years relative to feature sets. The chasis does off real reduntency like dual RSMs which is much better than trying to use HSRP or the like on the stackables.
MikeS
Home of the book "Network Security Using Linux"