Making a wireless clicker to use in presentations, suggestions?
Well, you'll need a transmitter and a receiver :-).

Infrared
You mention disadvantages like limited range and having to direct the transmitter, and it will depend on the setting how bad these are. Obviously a large auditorium will be more of a problem that a 20 seat room. 

Suppose we go for IR, what do we need? There's the protocol and a few codes (at least next and previous slide). For the protocol you can choose an existing one, and even use existing codes, but if you make both transmitter and receiver yourself you can also devise your own protocol. Advantage: you can make it as simple as you like, especially regarding decoding, which is more complicated than sending. One of the most simple protocols is Pulse-Pause Modulation, where you send a series of fixed-width pulses, and encode the bits in the time between pulses.

Transmitter
This is the easiest. Basically a microcontroller, a transistor and an IR LED. Microcontroller is asleep, and wakes up when you press a button. Start sending the modulated code until button released and go back to sleep. The finished product tomorrow morning on my desk, OK? ;-)

Receiver
An IR receiver is quite complex, and you don't want to make this yourself. Especially AGC is no fun. So we buy a receiver module, like from Vishay. This gives you the decoded signal which can be used directly by the microcontroller. Note that when the IR receiver modules don't receive a signal the AGC will lock to the noise and output that: a lot of garbage. But no worries: when a code is received this is as clean as can be, no noise whatsoever.



RF
The alternative is RF. You can use the same protocol and codes, and the transmitter will look almost the same. Just output the (unmodulated!) codes to an RF transmitter instead of the IR LED. 

RFM70 modules are small, cheap (around 5 dollar IIRC, I think Wouter knows them well) and easy to interface.