I'd prefer option 3 ! Its neither 1 or 2 really, more a hybrid.
What happens in option 2 is your company gets bigger and you end up with many many little cheapo switches under every block of desks. Then you find looped cables take out your network when some joker starts messing with the wires. You'll also spend you whole life on your knees messing with switches in a hiddeous pile of wires under people's desks.
Option 1 take a little more thought, but is better overall, however you normally dont run cables from pc's to the server room in one hit. What you likely want is:
A group of cat ports under desks (typically under the suspended floor if you have one) - 3 per person is usually enough to allow for voip phones and laptops
Each of those ports under a desk is wired to a patch panel in a cabinet (one per floor say)
Also in cabinet is the switch(es), you patch those floor ports into live switch ports as needed. Make sure you label up the patch panel fully !
Uplink the switch(es) to the server room.
I've seen this done several times and it worked out really well. When people join you just wire in the floor ports to the switch, and it makes it easy in the future if you migrate to VoIP phones or want to segregate the network, and when people move desks.
The key is to make sure you have a fair number of ports (employees x 3 say) all wired to the patch panel. That way you can pick and choose what you make live, and avoid the hundred mini switch nightmare of option 2.
In your case you may need to alter this slightly to take the cables up and into the roof space, but its one of those jobs where a weekend of work will make your life a million times easier.
I've also had the "everyone has a switch under the desk" situation (not by choice) and you'd be amazed how bad the wiring nests get after being kicked by feet for a few months.