For a trip in Sept to Croatia, I will be using public transport. I am looking for a good small group tour operator who offers day tours from:

Dubrovnik - Mostar
Dubrovnik - Montenegro

Split/Trogir - to Plitvice
Split/Trogir - to go whitewater rafting

I also plan to kayak while on HVAR and Korcula.

Any recommendations would be appreciated.

The bus service is very good and would be my way to tour. All your information is here, www.autobusni-kolodvor.com
If you still want to use organized tours, then wait until you get there.

When I was in Dubrovnik in 2004, I did a day trip to Bosnia (Medugorjie). I booked it from an excellent travel agency located in the main square of the old city (the square is very small, literally 'a square' so the agency is easy to find). It was not expensive, travelled in a fully serviced very comfortable coach, and included frequent stops for refreshment. I recall that they offered many other day/2 day trips as well including to some of destinations you are interested in.
Its obviously been a while but I'll try to find the name of the agency. If not I can recommend that you book once you get to Dub. It will likely be cheaper and you'll have no problem booking on a walk in basis day before.

Same goes for Split, but you may be rushed going to Hvar and Korcula for only a day trip. They are both very charming islands and towns. I visited both while staying on Brac for 4 days.

thanks so much Mathieu. I have alotted 2 nights HVAR and 2 nights Korcula.

So you didn't want the bus schedule?

plenty to do on hvar
we had a hire yacht and stayed two nights
got a car and still didnt visit the whole island
gee it is pretty!

Companies running tours from Dubrovnik to Mostar, Montenegro and other places are...

www.adriatic-explore.com

There is also Atlas and Elite travel agencies, used by many people here. If you google them you'll find their websites as I don't have them to hand.

Yes LittleVicky - the bus schedule is needed for either Zagreb-Plitvice or Split-Trogir part of the trip - itinerary still a work in progress, so thank you.

JT : It was Atlas Tours that I booked with.
Very good service. They even called me at home here in Canada the week before I left to confirm a flight booking they had made for me from Zagreb to Dubrovnik. I had the ticket waiting for me at the airline counter when I eventually arrived in Zagreb. I promptly gave them the rest of my business for tours, car rental and even a last minute change in accommodation, upon arrival in DUB with no regrets. They were very good and very pleasant.

Thanks so much Mathieu!

Atlas isn't small but I took two of their tours and REALLY enjoyed them. I took the Peljesec Penninsula (spelling?) wine tour. It was great.

I have been in touch with Atlas and unfortunately they only run the Plitvice and KRKA and certain days of the week - and my luck, days of the week that don't work for me. One downside to planning your own itinerary! I'm going to contact some other agencies on the off chance I can find someone running it on 5 Sept 09. Not sure I want to rent a car to do a day trip from Split to Plitvice?