We've found that lodging is often the hardest part of planning our trips, especially with our European trips. Since European hotels often have lower guest limits (usually 2 to 3 people per room), we either have to book several rooms or find a hotel offering a "family" style room.
I've found several sites that have offered great deals and have accommodations that meet our needs.
Lastminute.com (a British based site)
Another thing we have discovered about lodging is that you should always call the hotel directly. Often times we've been able to book one room because our children are young, by calling the hotel and speaking with a rep. I've also been able to get additional "amenities" by speaking directly with a hotel rep. It is amazing what you can do by talking to someone!