For me and my family, the differences between a package and a room-only reservation are minimal and meaningless.
The differences are in what you get included, what you can buy additionally, and terms of payment.
INCLUDED IN A PACKAGE:
A package, by definition, is resort stay plus park tickets (in any amount you choose ... it doesn't have to match your resort stay). In addition, there are several small freebies, the ones listed above by mickeystoontown. For my family, the only one we'd ever use is the free PhotoPass photo. Since we don't do mini golf at WDW (we live in a sort-of mini-golf capital) and we don't care to eat at Planet Hollywood, those freebies are meaningless to us. The luggage tags are cute enough, but to me they are pretty much in the "who cares" category.
Now here's the very weird thing that most people don't seem to realize.
Even when you book a room-only reservation, you can still include tickets when you make your resort reservation. When you purchase your park tickets this way, it is part of your reservation and you will automatically get them encoded on your room key at check-in.
Regardless of package or room-only, everyone staying at a WDW owned-and-operated resort is entitled to free airport transfers and automatic luggage delivery (Disney's Magical Express). DME is free, but separate reservations are required.
WHAT YOU CAN BUY ADDITIONALLY:
If you want to buy the
Disney DIning Plan, it can only be purchased as part of a package. People doing a room-only reservation or people not staying at a WDW owned-and-operated resort aren't eligible to purchase the DDP.
Again, for my family, the DDP is meaningless. By choice, we eat only one or 2 table-service meals each trip. We aren't interested in a table-service meal every day (part of it is that we hate running on a schedule during any vacation, so the idea of planning and timing our activities in order to make it to an ADR just spoils the very idea of a vacation for us). We are perfectly satisfied with counter-service for most of our meals during the week. And the last time we were there, my wife and I were training for our first-ever half-marathon ... we weren't about to assault our bodies with red meat and fried foods, and there is a large variety of healthy and yummy counter-service food, you just have to know where to find it.
TERMS OF PAYMENT:
When you book a package, you have to pay a $200 deposit within 14 days of making the reservation. The balance is due no later than 45 days prior to your arrival day. If you book air travel through Disney, you must pay 100% of that cost at the instant you make the reservation.
When you book a room-only reservation, you have to pay a deposit equal to one night's room rate + tax within 14 days of making the reservation. The balance is due no later than the time of check-in. Despite what someone alluded to above, you
can pay early on a room-only reservation. Disney is more than happy to take your money before you are required to pay it.
So for my family's likes and dislikes, whether we book a package or a room-only (we've done both) is pretty meaningless.