There aren't a lot of hotels in Melaka, although there is a good range of accommodations, from inexpensive guesthouses to five star properties. As with any destination, one important decision is what area to stay in. For Melaka, I think it's best to stay as close to the historic area as possible. Several of the old shophouses in Chinatown have been converted to hotels and guesthouses. Among these, the Puri Hotel is probably the best of those that can be booked through the on-line sites. The Baba House is also acceptable, if cost is more important than a window. Two places in this area worth mentioning but not listed on the independent booking sites are the Courtyard @ Heeren and Heeren House.
If these small places don't appeal, there are several larger hotels outside of the historic area to choose from. The Majestic Malacca is probably the top end of the hotel offerings. Built around a restored 1920s mansion, the 54 new rooms offer all the mod. cons. while remaining true to the 1920s theme. The hotel is built right on the river, a long walk or short boat or taxi ride from the historic area. Lastly, there's the Holiday Inn, built right on the ocean front with a long 'entertainment' pier attached. It's a short walk to St Paul's Hill from the hotel, although the trip involves crossing a busy wide street (which you can walk under a short way from the hotel).
If you don't like my choices, you can use the search box below to use HotelsCombined to find the best rates by searching dozens of sites at once.