I was just in Sabah, Malaysian Borneo in December. Some cool things to do are climb Mt. Kinabalu, the tallest mountain in SE Asia (not including New Guinea) which I've heard is a relatively easy climb because they have guest houses half way up for you to stay the night. There are a lot of parks in Sabah, but call ahead to see if any Rafflesia, the largest flower in the world (1 meter across and bright red-orange), are in bloom. They live for two years and only bloom for one week so you have to get lucky. Kota Kinabalu is a dirty, unfriendly city in my opinion
Go snorkeling or scuba diving! Malaysia has some of the best spots in the world, especially Pulau Sipadan which is considered by many THE best in the world. Google it for images and see what I mean. The reefs aren't the best but the sea life is. Three tour operators have a monopoly on running tours. Getting around, I highly recommend AirAsia, a Malaysian low-cost airline, over buses because the roads are tight and windy, and getting across Sabah can take 8-10 hours. My favorite town was Sandakan in the north from which you can take excursions to the Orangutan Rehabilitation center (entry fee is 10 ringgit plus 30 for a camera pass, about 12 USD total) and Turtle Island. Turtle Island is an island with a beach where lots of sea turtles come up during the night to lay eggs, but call ahead to see if it's the right season. It wasn't while we were there. You have to book a reservation at the hotel too.
I don't know what kind of accommodations you are looking for, but a sweet backpacker hostel I stayed at in Sandakan is called Sandakan Backpackers. It's a new building with individual rooms, very cheap and clean, and located right on the waterfront, basically in the middle of the city. The people who run it are also friendly and speak English.
Don't expect Malaysia to be cheap like a third world country, because it's not. GDP per capita is about 6,700 USD, very high for SE Asia. And they always jack up prices for Westerners, making no distinction between student backpackers and wealthier businessmen. Haggle when hiring a taxi (except at the airport where prices are usually fixed) or buying anything where the price isn't listed. But don't spend too much time or you'll get frustrated and waste a lot of your time and energy. If a cab says 30 MYR, offer 20 and you'll probably get 25. It's not much but it shows them you're no idiot. You can also ask the people at the hostel what price recommendations. Don't drink the water.
Malaysians (or at least Sabahans) are friendly and will smile and be happy to talk with you. Smile, relax and enjoy the culture.
I never worried about or got any harassment for being an American.
LondonOllie, we may go independently as well. How did you find the connections - did you fly / bus / both? Our primary goals will be to get to see Pinnacles, the Oranguatns in their natural environs, and find the clouded leopard. We will only have about 2 weeks so dont' want to waste much time sitting on buses for days...
I'm assuming you both went to the Malaysian part of Borneo and not the Indonesian part?
If you only have two weeks, you can probably do what you want, but you may need a little planning as opposed to winging it.
Do you know which bit of Borneo you want to go to?
I presume you are thinking of Sabah or Sarawak, and not Kalimantan.
Some of the busses were scary, but that is the norm in that part of the world and kinda part of the fun really.
Just go spend a Sunday at the bookstore and find a few books to see what you can find out. Also you can always find the message boards on LP and others.
I was there almost 8 years ago now, so it's probably changed a fair bit.
2 weeks to do it independently as I say...you can do it, but you will just need to plan ahead a little bit. Finding accommodation shouldn't be a problem but the connections and a rough idea of where you want to head and timeframes are probably key before you set out.
If you want to see the Orangutans, try to go to a place where they don't let you get too close. I know you may feel that kind of defeats the point, but if you can see them in their natural environment where you don't have people 'petting' them, that's the best thing for the animals.
The Orangutan Rehabilitation Center near Sandakan is a good place to see them because they have a feeding platform about 10 meters from an observation deck built a meter above the jungle undergrowth. Very cool animals.
I wouldn't want to do the "petting zoo" viewing, I much prefer to see them in the wild, in their natural habitat. Thanks for the info on the rehab centre, I read about it but my initial thoughts were that it would be a petting zoo...