-damage to tenant's property (not on me, since tenant should have made sure they were covered by renter's insurance, correct?)
-tenant's lost time at work dealing with the initial incident and subsequent times they left early/late to let in workmen (again, not my concern as long as I make myself available for this now that the tenant is at the end of their rope?)
-reduced usage of the house with a large portion of the subfloor exposed and fans running for a few days
-increased water/electricity bill from the incident
-Damage to their property: I agree they should have made adequate provisions to cover this with their own insurance. If the loss ammt didn't exceed their deductible that's their problem, I don't think you owe them anything on this one.
-Lost time: Eh...I have to side with the tenant on this one. Whenever I have had work done at my rental, I have asked if the person would normally be home. If so, and they have no issue letting the workers in, then no problem. If they've said they would be at work or otherwise unavailable/uncomfortable, I have always made provisions for my wife or I to be there and let workers in ourself...i feel morally this is a landlord issue. I don't know how much (if any) you might 'owe' them for doing this, but I don't think it's just 'all good since you can do it now that they are fed up'. Perhaps this one can be handled with a decent bottle of wine or something to thank them for being accommodating with the promise that you will handle it going forward.
-Reduced usage: I feel some compensation is due in rent reductions...exposed subfloor is not totally horrific, but they are paying $XXXX to lease your place in the condition presented, not with tore up floors and loud fans running part of the time and workers traipsing in and out for a month and a half. When the AC went down in my rental and it took almost a week to order the required parts and get it fixed, I comped my tenants the whole week of rent for suffering through that sweltering time of year, which i'm sure was miserable. This isn't the same persay but if I was the tenant I would expect some comps. Its like someone renting a nice car for the week and then you telling them as they pull away...oh yeah, btw the windows don't roll down and the stereo doesn't work, good luck...the car still 'works', but it's not what they expected and paid for.
-Increased bills - Side with the tenant again on this one (but no idea what 'magnitude' we're talking). Regardless of what the lease/law says, in no way morally should they be held responsible to pay for the electricity to run the fans and that the workers use for running tools for repairs, or however much the leak may have increased the water bill (I had an irrigation line blow last year and it jacked my bill for the month by almost 100 so it may not be 'chump change'). Whoever suggested crediting the difference between this period last year and this year to account for the extra and adjust for seasonality was spot on.
Good luck, I know how trying these things can be in rentals. On one hand you want to be a good person and do right by your renters...on the other it's hard to keep taking monetary punches to the gut and writing big checks. Just remember, this too shall pass.