Since in both cases you are well within the reach of multimode fiber, it makes no sense to look any further, as it is the most cost effective solution unless you need 10 gigabit performance.

As to what switches to use, there are a lot of variables once you get past the basic requirement here of having of having two optical ports on the one in the server room, and one optical port for the other two. Other considerations are how many ports do you need in the server room, and in each of the two departments. Then features, performance, and reliability factors come into play, along with budget.

If you don't need a lot of ports, and you are looking at normal office levels of traffic, 3560's might be a good choice. You could put a second one in the server room, and duel home the servers and department switches to them to add redundancy. That would make a single switch failure unlikely to take out the whole network at one time. One the other hand if you need hundreds of ports, have a mission critical situation, or expect intensive levels of data traffic, then you will need to look at high end switches such at the 4500 and 6500 series.