Hi Craig,
what Cor says about Sipadan is true. It's closed now but you can dive it from Mabul and if you're in Malaysia you really shouldn't miss it. As for the diving it's stunning. I went a couple of times before it closed and it's simply the best diving I ever did. Us divers tend to exaggerate at times but I swear to God over the course of around 50 dives I've done on Sipadan I have never once seen less than half a dozen turtles and half a dozen white-tips at minimum on every dive. Often there were so many as to lose count. During those 50 dives on Sipadan I've also seen lone and schooling hammerheads, leopard sharks, grey reef sharks, mantas, mobulas, various stingrays, masses of barracuda, masses of jacks, and all the usual reef fish and critters. The place is simply awesome. If you can you should also try and find one of the few dive guides who know the turtle cavern under the island and can take you in there (don't go in there on your own, you can easily get lost and die - you wouldn't be the first) because it's quite an experience.
As for another diving option in Malaysian Borneo you should also consider Layang Layang. It's all wall diving of the highest order. You can only reach the island by plane from Kota Kinabalu but it's worth it as it's remoteness means utterly pristine walls and topreef with big pelagics and 30-40m visibility. It's particularly well known for hammerheads. A typical profile means dropping straight down to 37-38m and swimming away from the wall into the blue to look for hammerheads. 5-8 mins bottom time then ascending back towards the wall to rejoin it around 15-20m and drifting along it. Fantastic place also because the resort holds about thirty people max and it's too far for any dayboats so you always have the dive sites to yourself.
Finally a word of warning about Sepilok. It's a rehabilitation centre and the Orang Utangs are indeed cool but you see them being fed for about an hour or so and then there is bugger all else (except for the war memorial) in the vicinity. Instead you could spend a few days in a jungle camp (I recommend 'Uncle Tan's' if you don't mind living with only the barest basics). That way you get to really walk through the Borneo rainforest and see real wild animals in their own environment.
Also, somebody else mentions climbing Mount Kinabalu. It's a great trek to the top but it's far more demanding than they lead you to believe because of the altitude and the early start (full day, then a few short hours sleep in a freezing cold hut, then a 2.30am start so you reach the summit for sunrise). I am of average fitness and I did make to the top for sunrise but by the time I got back to the bottom my legs were gone and I couldn't walk without a stick. To properly enjoy the Kinabalu climb you need slightly better than average fitness. It's worth it but it's hard work.
Hope this all helps and I hope you like Malaysia. It's a great country.
Cheers
Marco