We usually begin researching our shore excursions up to a year in advance, or as soon as we book the trip.
The first thing we do is check the ship's excursions. Although booking may not be open for your cruise until 120 or 90 days before, you can see the typical list of excursions for your particular ports. This gives you a very good idea of the most common tourist attractions at that port.
Then we will check the major consolidators, such as portpromotions.com, shoretrips.com, and toursbylocals.com. Frequently they will have some interesting suggestions for private tours going places that the big ship's tours cannot go, although in other ports they just repeat the ship's list, occasionally for a few dollars less.
Then we go to the boards. This one is excellent, of course, and Frommer's and TripAdvisor also offer great suggestions for attractions and operators.
Finally we google <port> day trips or <port> shore excursions and will often get some off the beaten track ideas.
So, with a pretty good idea of what is offered in the port and usually a list of recommended operators and guides, we start to figure out what we will do in each one.
The ship's excursions are often very good, and the ship frequently has the best guides, the best transportation, and the best reservations all tied up. Taking the ships trip, such as whale watching in Alaska or wildlife in Australia can be an excellent idea, convenient, easy, and safe.
In many cases, we don't want to be crowded onto one of six buses from the ship all going to the same cathedral or museum, or we have places we want to go not offered by the ship, or we want to concentrate on one particular place for longer than the ship offers, or we want to be sure that our slight mobility limitations are accomodated, or we just feel like being independent! Then we will book with a private guide from one of the sources listed above. This worked wonderful for us in St. Petersburg, Egypt and Borobodur Java for example!
When you book privately you do have to be aware that YOU are solely responsible for getting back to the ship on time, and for assuring that your tour stays in safe tourist areas. Most reputable operators are very well aware of this.
Having made up our minds, we will book the things we really want to do (like helicopter flights or the Hermitage) as far in advance as possible -- 90 to 120 days for the ship, and as much as 9 months in advance for popular tour operators like Orca Enterprises in Alaska, Captain Marvin in the Caribbean, or DenRus in Russia because they book up fast. In some cases we have boarded the ship and the shore excursion office was already posting that half the tours were sold out.
For good examples of how we like to mix ship's excursions with private guides, check out http://www.bully4.us/alaska2010.html
, or http://users.elite.net/thehalls/maasdam.html
Have a GREAT cruise!