You basically have three options:
- Hot mirror in front of sensor (e.g. stock camera)
- Only good for visible light, IR exposures are possible with a lens-mounted IR filter, but exposure times are on the order of minutes.
- Cold Mirror (e.g. IR Only filter on sensor) - Camera is only good for IR Photography.
- If you have this professionally done, (or are into DIY), this will involve recalibrating the focus sensor for the new filter and your lens's IR focusing offset.
- This is definitely the easiest to use - the viewfinder remains useable at all times, and the AF will always set the focus correctly.
- All-Pass filter on sensor - Camera is good for IR and Visible lights, but there are caveats to using in either mode.
- You will have to always have a hot mirror (IR Filter), on the front of your lens, or you will get unusual colors/overexposure from IR light in visible light photos. This will likely entail buying a hot mirror for every lens you own.
- Shooting IR requires a cold mirror, and it has to go on front of the lens. Therefore, you will not be able to use the viewfinder when shooting IR.
- The camera's AF sensor has a separate IR Filter. Therefore, AF will not work when a cold mirror is on the lens. Every IR shot will have to be composed and focused in visible light, and then you will have to mount the IR filter to the lens, and take the shot.
- You can calibrate the AF sensor for either visible light or IR light. In one shooting mode, you will have to dial a certain amount of focus compensation in. This is simple (basically, you just shift the focus ring by a known number of degrees), but you have to do it ever time.
I strongly recommend having separate camera bodies for visible and IR. A clear (allpass) filter involves many compromises, and is generally a pain in the ass. the only reason I think it could be a good idea is if some bizarre situation means you can have only one camera body with you.
A note on focus correction:
The AF can be corrected for one or focus offset. This is why places like lifepixel ask for you to send the lens you plan to use the camera with to do focus correction. Basically, the way it works, is the lens either front or back-focuses IR by a certain percentage (this is what the IR focus mark on some lenses shows).
Correcting the focus involves basically inserting a corresponding amount of front or back focus into the AF system by physically moving the AF sensor using it's adjustment screws (e.g. how the focus is tuned at the factory, and what they change when you send in your camera to have front/rear focus issues corrected.
The end result is a camera that always front or back focuses by a certain amount. However, this focus offset is the opposite of the IR focus offset, and the two cancel out.
The camera is still focusing using visible light. However, because of the offset, it ends up with the focus set correctly for the lens it is compensated for.
Therefore, if you use a different lens, with a significantly different focus offset, or a telephoto where the focus offset changes over the zoom range, it will be blurry. However, you can get tack-sharp results with the original lens.
The only way to have a IR camera focus correctly with any lens in IR is to remove the hot mirror from the AF sensor, and no one on the market does this service. I removed the hot mirror from the AF sensor on my D80, but it's a really involved process, and I nearly broke the thing in doing so (it's glued together).
In the comments on imre's answer, Matt Grum seems to be confusing the sensor cover glass with the sensor filter. These are separate elements. There are some cameras that combine the two (The Sony Alpha A200, at least), but these cameras are basically impossible to convert, unless you have access to a cleanroom. All the other cameras have separate pieces of glass.