I would send out an email explaining the situation and when the migration will take place. Be sure to be positive about the situation. Discuss what features your services have and how the user will benefit from your full attention.
DoMeric, that is a good idea. anything that makes the customers feel welcome is going to only help the transition. Depending on the number of sites, the big accounts might deserve a phone call just to introduce the new company. It's nice for the customers to hear a voice that there is real people behind it.
I would think that Most importantly you must make them feel at home. Give them priority for support during the first few month so as to make them feel important and also some incentives to keep them stay.
Once they have settled down, there should not have much problem continuing provided your service is good.
When I purchased another host last summer/fall and migrated 90+ accounts to my servers, we did our best to communicate with the customers. The more we communicated, the more comfortable they were. If you can send personalized emails and make them realize that there is a real person behind the company that is taking over their account, they will be even more comfortable. The last thing they want is to be moved to a host that thinks of them as just another number.
I have better relationships with some of the customers I aquired than customers that signed up with me directly because of that high level of communication that we had. They know that they can email or call me directly, and are now more loyal to me than a regular Joe Hostee who signs up on my site without much communication between us before hand.