After just having spent a full week reviewing tours of Israel I realize the following:
Many tours are geared for particular clients. For example, there are some that seem to have far more Christian sights, some for far more Jewish sights, some that have prayers affiliated with each sight, some that request that participants wear "proper" attire and seem more orthodox, some that are very light and general, and some that are more historic and archaeological in focus.
The price differences are significant and may range from $4500. for two people for 11 days (which is really shorter since they count the day of departure) to much less for a backpacker's tour to much more for groups such as Tauck or even going on your own with a private tour guide/driver.
The best time of year weatherwise seems to be Oct. Nov. and spring- around April. Since April is Passover and would limit food options, I ruled out April and decided that optimal for us would be the second half of October or the first half of November and in fact the tours are often sold out for that time of year by now.
We decided that we prefer to go non stop rather than changing planes with long wait times so we paid extra for better flight times. We also decided that we prefer the historic/archaeological perspective with more Jewish sights than Christian ones but definitely do not want any orthodox leanings, clothing rules, or the primary emphasis on participating in religious events. We also felt that if we are joining a tour group (very unusual for us as independent travelers) that we also want time to travel and explore by ourselves. So we compromised and picked the King David Gate 1 tour through vacations to go with upgraded non stop flights from NY and with 6 additional free days after the tour ends to explore on our own but then use their flights home. We think this will allow us to go to Eilat if I want to snorkel in the Red Sea, return to some favorites for more time, visit Haifa which is not part of the tour, and shop more at the end rather than dragging purchases around with us.
You need to make some decisions about religiosity, focus, time period, size of group, places you want to go, types of flights, what you are prepared to pay, and which are your priorities in terms of where you want to go and what you want to see. Go to your local library and take out some guide books and read and skim them. Then it will become clear to you which are the right tours for you.