The Pan Pacific aiport hotel is good for an overnight stopover- connected to the terminal by a bridge so v convenient. Has a swimming pool and good food and saves the hour's taxi journey into KL city centre.
In town there are loads of nice places to stay- Bukit Bintang or KLCC areas are central. There are usually good deals on Agoda's website. The JW Marriott is my current favourite- comfortable rooms, nice pool, and several great restaurants in the mall next door (Starhill)- Thai, Lebanese, Malay etc- all can be ordered on room service also. Traders hotel in KLCC is excellent too- with good views of the towers from your room! Also recommend the Millenium, Prince (can book a serviced apartment there, might be good with a family) and the Mandarin Oriental.
Activities wise- the bird park and butterfly park at Lake Gardens are worth a visit, as well as Bukit Nanas rainforest reserve. Also the aquarium and petrosains discovery centre in klcc (which could be combined with a trip up the twin towers to the viewing bridge).
The Islamic Arts museum is excellent, also interesting to walk around chinatown, maybe the Central market, and the craft centre on Jalan Conlay where you can see various artists at work. If wanting to burn off some energy, or for a wet day, there's an indoor climbing wall, camp 5, at 1 Utama shopping centre. The Royal Selangor pewter factory is another rainy day option- children can make their own bowl etc.
Depending how much time you have, Penang or Langkawi would also make great side trips for a couple of nights- just short flights away, and a nice contrast to the city.
Hope you have a great trip.