From Whindoek to Lilongwe, the easiest way would be to fly from Whindoek to Johannesburg (with South African Airways, Air Namibia or Kulula/Comair), stay overnight in Johannesburg and to fly the next day from Johannesburg to Lilongwe with South African Airways. South African Airways has also flights from Johannesburg to Blantyre (in this case, you would need also to stay overnight in Johannesburg). Another alternative from Windhoek to Lilongwe could be to fly with Air Namibia from Windhoek to Lusaka and with Kenya Airways from Lusaka to Lilongwe (take a look at the schedules of both airlines to see when they fly those routes and to see if you can easily combine them).
From Lilongwe to Entebbe you can fly with Kenya Airways (changing planes in Nairobi) or with Ethiopian Airways (changing planes in Addis Abeba).
If you don't bother to change the order of the countries, you can fly with South African Airways from Whindoek to Entebbe changing planes in Johannesburg without needing to stay overnight in Johannesburg.