I will be in Bali for 12 days but I will be taking a side trip to Borneo via Surabaya on a domestic flight. If I pay the $25 fee coming in, what other fees will I need to pay going to Surabaya and back?

Domestic airport tax in Bali is IDR 50.000, so about US $5. Other domestic airports charge similar amounts. Needs to be paid in cash in Rupiah.

International departure tax is IDR 150.000.

Just want to update this post -

There is now only 1 visa on arrival - it is a 30 day visa and costs $25 USD - they do accept other currencies but only notes - and give change in Indonesian Rupiah.

There is an option to extend this visa once you are there but it is not easy and takes a lot of hanging around etc.

If you are going to stay for more than 30 but less than 60 days you can get a 60 day visa from your local embassy or consulate before hand.

Some flights on Garuda do have Immigration service on board - this is a world first - Sydney, Tokyo and Osaka I think are the only ones.

You pay your $25 when you check in - separate counter - then after the meal service the Immigration people come thru - one per aisle and stamp you into Indonesia - they then issue you with a laminated card like a boarding pass - that says Immigration cleared - and you just go to the precleared line - hand in the pass - and go collect your bags - clear customs - (xray) and off you go to enjoy the delights of Bali (this happens on flight to Jakarta from Sydney and some other selected cities as well

Depends on where you do it. I extended in Ambon last June and it was dead easy. Didn't even have to go myself - but that is probably not an option if you don't have some local contacts. But the charge in Ambon was really only $25, no extras, no "tips" (except for the driver that I sent).

I understand that the process tends to be a bit more tedious in Bali. So on my last overstay in January I didn't bother to renew and just paid the "penalty" (US$ 25 per day) on exit. They do count the arrival day(!). However, this option is not for the frugal. Renewal is only US $25 for a whole month, so that's definitely the cheaper option. In Bali it may require some extra "tips" on top of that.

As adampenrith indicated, getting a 60 day visa may be the best option, if you already know that the 30 day visa won't be enough.