From the American Association of Museums web site:
Alexandria Zoo (as of 8-31). AZA reports that the Zoo is fine. They had no animal loss.

Audubon Nature Institute (as of 8-31). AZA reports that the staff of the Audubon Nature Institute is safe. The physical plants at both the Zoo and the Aquarium suffered little damage. The staff will continue to assess the impact on the animal collections at all Audubon facilities. The Audubon Center for Research of Endangered Species (ACRES) lost one whooping crane but the remaining animals at the facility are fine. The area has not been flooded but there are some leaks at the Research Center. Four animal keepers were flown in by helicopter. At present, they do not need food or water.

Aquarium of Americas (as of 8-31). The Palladium-Item reported that the Aquarium, located on Canal Street a few blocks from the New Orleans' French Quarter, lost only one fish and he had been sick before the hurricane hit.

Beauvoir, Jefferson Davis's home (as of 9-2). The Clarion Ledger reported on 8-31 that Beauvoir, located in Biloxi, was "virtually demolished." George Malvaney reported that he visited Beauvoir on the evening of 8-31. He said the bottom floor of the house was gone, the upstairs badly damaged, but that many artifacts were intact. He said artifacts have been temporarily secured. On 9-1 Greg Biggs reported from Larry McCluney that approximately 65% of the main house still stands, although the porch, windows, doors, columns, & front porch are gone. The first floor of the library is gone, but Davis's papers had been moved upstairs and survived. The small home where Davis resided survived. Other buildings, such as the gift shop, are gone.

Biedenharn Museum and Gardens (as of 9-2). Ralph Calhoun, executive director, reports that the museum and garden are fine. 

Birmingham Botanical Garden (as of 9-1). AABGA reports from Fred Spicer that "Mother Nature has done some pruning" but the garden had no structural damage.

Birmingham Zoo (as of 8-30). AZA reports that the Zoo is without electricity, has some trees down, but suffered no animal losses.

BREC's Baton Rouge Zoo (as of 8-31). AZA reports that the Zoo has electricity now. There are lots of trees down, but no animal losses. They are already working on clean up.

Danzler House (as of 8-31). Located in Biloxi, the house had just been remodeled to house a Mardi Gras museum. TheDay.com reported that it was destroyed.

Davis Planetarium (as of 8-31). The Clarion Ledger reported that manager Gary Lazich said the planetarium had a small leak around the outside but no significant damage.

D-Day Museum (as of 9-1). Caroline Kennedy, Director of the West Baton Rouge Museum, reports on communication with Kenneth Hoffman of the D-Day Museum. Housing for staff is the main need.

Gulf Coast Exploreum Science Center (as of 8-31). The Mobile Register reported that an estimated 5 feet of water came through the front doors. The original exhibit gallery was flooded with about an inch of water, but was under renovation anyway. Tim Pula, Science Coordinator, confirmed that the exhibit gallery was in a tear down phase of a major rework, so the damage was minimal. The museum had planned to be closed for a week, after Labor Day, for maintenance and Tim expects the museum to be up and running fine after that.

Jackson Zoo (as of 8-30). AZA reports that the Zoo suffered very slight building damage and has about 35 trees down. There was no injury to any staff or animals. About half of the zoo has power. They will be closed for about a week while they clean up the trees.

Louisiana State Museum (as of 9-2). Kacey Hill, Public Information Director, states that early reports indicate that the Louisiana State Museum's 9 historic French Quarter properties have sustained varying degrees of modest to severe damage as a result of Hurricane Katrina. Curatorial staff has conducted a preliminary survey of both facilities and collections for immediate stabilization purposes. Continuing assessment of conditions is underway, but it is too soon to fully realize the extent of the site repairs and collection treatment needed. Museum officials have received numerous calls from other institutions offering assistance, and look forward to accepting these generous offers in the weeks and months ahead. For more information, contact the Louisiana State Museum-Baton Rouge at 225-219-0729.  

Marine Life Oceanarium (as of 8-31). The Baltimore Sun reports there is an empty space where the Gulfport aquarium used to be.

Miami Museum of Science (as of 8-31). ASTC Informs reported that the museum weathered the earlier landfall of the hurricane, sustaining damage to the Wildlife Center, but relatively little water penetration. President Gillian Thomas says the museum has already reopened, having been closed on Saturday and Sunday during power outages and clean up of fallen trees and damaged structures.

Mississippi Museum of Art (as of 8-31). The Clarion Ledger reported that the covering over a skylight that was to be repaired blew off. Director Betsy Bradley said that as a result leaks are recurring and ceiling tiles are down in the atrium area. The art was removed prior to the storm and was not damaged. Bradley said the museum will re-open very soon.

Mississippi Museum of Natural Science (as of 8-31). The Clarion Ledger reported that the museum dodged major structural damage but not a power outage and water leaks. Emergency personnel scrambled to find diesel fuel for its generator to keep the 100,000-gallon aquarium system operating. Electrical power came back on Tuesday afternoon. The museum planned to reopen for visitors on Wednesday. 

Montgomery Zoo (as of 8-30). AZA reports that the Zoo is without electricity, had some trees down, but suffered no animal losses.

National Park Service sites (as of 9-1). The NPS's Morning Report has updates on the recovery efforts in its parks and monuments, including the Everglades NP, Dry Tortugas NP, Gulf Islands NS, Jean Lafitte NHP, New Orleans Jazz NHP, Natchez Trace Parkway, Cane River Creole NHP, and Natchez NHP.

New Orleans Museum of Art (as of 9-1). The Times-Picayune reports that the New Orleans Museum of Art survived Hurricane Katrina and its aftermath without significant damage. Six NOMA security & maintenance employees had remained on duty during the hurricane. FEMA wanted them to move to a safer location, but there was no way to secure the artwork inside so the staff continues to stay on site. Museum workers had taken down some pieces in the sculpture garden before the storm, but a towering modernist sculpture by Kenneth Snelson was reduced to a twisted mess in the lagoon.

Ogden Museum of Southern Art (as of 8-30). Fran Huber, Registrar with the Louisiana State University Museum of Art, reported that the Ogden was fine on Tuesday, but she had no news since the levees broke.

Old Capitol Museum of Mississippi History (as of 8-31). Cindy Gardner, Field Services Curator, reported that the museum had a third of its copper roof blown off, with water then pouring into an exhibit area and a storage room. Staff has been working on moving artifacts from one side of the building to the other. They have hundreds (if not more) of wet artifacts and some that are completely ruined. More information is available from the Clarion Ledger.

Rosemont Plantation (as of 9-1). Site director Percival Beacroft reports that the site is all right and in no danger.

USS ALABAMA and USS DRUM (as of 9-1). Jeff Nilsson, executive director of the Historical Navel Ships Association, reported on 8-31 that the ALABAMA was listing eight degrees to port (toward the pier), but the USS DRUM is apparently in good shape. The concrete gangway has been critically damaged, while the airplane hanger suffered damage to all sides and the planes are in a pile. The Pavilion and Gift Shop both suffered damage. There are two feet of water in the Gift Shop. The ALABAMA web site can be found by going to hnsa.org and clicking on their link. The home page gives an index and by clicking on USS ALABAMA News there is an overview of the damage. On 9-1 the Mobile Register reported that the Battleship Memorial Park sustained extensive damage. The park's aircraft pavilion was apparently battered into a "total loss" but the dozen vintage warplanes are all repairable. The USS Alabama was listing, although it is not believed to have incurred any serious damage. Bill Tunnell, executive director, said the park could be closed for weeks for repairs but said a further assessment of damage was needed first. About 18 members of the staff and their families rode out the hurricane inside the battleship, as members have done voluntarily since Camille in 1969.

USS KIDD Memorial (as of 8-31). Jeff Nilsson, executive director of the Historical Navel Ships Association, talked with Maury Drummond, executive director of the USS KIDD Memorial in Baton Rouge. Maury said the ship suffered little or no damage and is expected to re-open within a week.