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Hello Mathias,
thanks for asking.
That really depends on what you want to do:
1) Apple Remote: 
Pro: 
+ small and slick
Minus: 
- you'll need additional hardware (if you go for it, my suggestion is 
to buy a Keyspan Remote for iTunes, excellent hardware) 
- not as portable due to the external nature of the receiver
2) WiiMote 
Pro: 
+ more buttons than the Apple Remote 
+ no extra receiver needed 
+ more cool features to come for the combo Remote Buddy + WiiMote 
+ more reliable (=> higher distance, virtually no transmission errors 
due to objects in the path to the receiver)
Minus: 
- needs fresh batteries every now and then (=> recharchables strongly 
recommended) 
- looks nice, but is not as small and slick as the Apple Remote (=> 
if you need to look smart at a presentation, a game controller is 
probably not the preferred device to control that presentation)
If you already have the Apple Remote, the price difference between 
WiiMote and Apple Remote should not be too great (=> check 
Amazon.com, they should ship both of the items for free IIRC).
Hope that helps.
To everybody else: Sorry for not following up yesterday and today to 
most of you. I'll reply to your postings tomorrow.
Best regards, 
Felix