Fixed function depreciation

Lotsa gfx cards nowadays don't even have fixed function hardware anymore. Rather, the calls are translated via the driver/runtime to purely programmable shader instructions.

I wouldn't worry too hectically about *having* to support purely programmable API just yet - because if Fixed function is exposed to you at the API level there won't be a problem it should just work.

That being said, many modern engines/games have already made the shift - the goal being to make ALL their pixels look good :) I highly recommend you look at GLSL for this goal - it really is great! :)

Fixed function API won't be completely useless for now though. It'll be good for rapid prototyping in the same vein that immediate mode is.

As for PBO's, you probably want articles on FBO's (recently written) and over here:
http://www.gamedev.net/reference/programming/features/fbo1/
http://www.gamedev.net/reference/programming/features/fbo2/

So did FBOs replace PBOs?

No, FBOs and PBOs are different;
FBO are framebuffers and used for drawing
PBO are used for data transfers and can be used to copy from an FBO to a VBO. The PBO spec has some examples at the bottom of it.

The next version of OpenGL is what's going to shift alot of things into a software abstraction level and won't be on the 'fast path'.

Most of the stuff which is going/being depreciated isn't a great deal of use in Modern OGL programming anyways, but it will still be around in some form for backwards compatibility.

This gives a good overview on what is planned for the future (the "future" being a spec release around June time this year infact).