First step is to loosen those things from the floor. Hopefully you can massage enough slack in the tubes and wires to allow moving them around a little.
Next is to break out the old wood. I like to use a reciprocating saw with a hook-tip blade to make plunge cuts into wood. The same could be done with a hand saw of the right size. Break up the wood with a chisel (or screwdriver) if a saw isn't an option. With this technique you can make cuts leading away from the holes in the wood and remove the wood in pieces. Basically you're extending the round hole until it reaches an edge of the board. Then the pipe isn't captive in a closed hole anymore.
Some of these Sawzall blades have the hook style tip I'm referring to (first and fifth from the left, and the one at the bottom).
Fitting new wood in is a bit of a trick, but it's more or less the reverse: take a solid sheet, make holes in the right places, then make cuts that cross the holes so that you can fit the wood into place in two or more pieces.
It can help to make a template of cheap material and transfer the pattern onto good wood when the template fits right. Cardboard and heavy paper are great materials. A roll of the brown or red builder's paper or rosin paper for protecting floors is perfect: cheap, rugged, and easy to manipulate with a knife or scissors. Keep in mind that templates can be made in many pieces and taped together: they don't have to look pretty, or even turn out perfect on the first try.