We too experienced some of the perks of being on our honeymoon when we visited in May, 1999. I believe that the common sense approach to this is to look for places that cater more to couples than the masses, and you should receive exceptional attention.
We were upgraded from a moderate resort to a one-bedroom villa at the Old Key West resort when we arrived. This resort is very quiet, and is secluded from the rest of WDW. Just what honeymooners need. We also got the free desserts at San Angel Inn and the Hollywood Brown Derby, as well as a congratulatory after dinner wine at the California Grill. Victoria and Albert's was also very attentive to the fact that we were honeymooners.
The coolest perk was visiting the California Grill on top of the Contemporary Resort. The staff put us at the corner table closest to the Magic Kingdom. Apparently, this table is very hard to get. There was a couple next to us that was celebrating their 25th anniversary, and they told us they had been trying to get that table for a really long time. From here, we had the best view of the Fantasy in the Sky fireworks of anyone. With the lights in the restaurant turned down, it made for a very romantic ambiance.
The thing to remember is that these sorts of perks are best when not expected. If you go in with that attitude, you will no doubt not be disappointed. Besides, you are way too busy enjoying that cool feeling of being a newlywed, as well as the whole Disney experience to let worrying about freebies distract you from the atmosphere of a Disney honeymoon.