Companies sometimes have to pay a fee to pay in a cheque with the bank, so it may be worth writing hundreds of small cheques out, just to P them off.
Alternatively, you could date it for the first day of the next financial year. What about getting a pen and spoiling the electronic account no/sort code information so they have to manually process.
When I was a student I was involved in a mass protest payment of rent to the Uni (as a result of an inflation busting rent rise). We all paid the entire amounts in 10p pieces (bear in mind hundreds of students paying in what I think was about �500 each) took the clerical staff hours to cheque and lug around.
Finally, I seem to recall that if you send a cheque for the wrong value and it is cashed, it is considered to be a done deal. This may be an urban myth, but it is worth trying out. Try sending one for 21p when it should be 21 pounds or such like. You never know!