For my 2003 Giant Sedona DX, I have made a few changes.
Slicker tires.
Had fork swapped for a rigid a couple of years ago. At the same time moved to a threadless headset, so I have a different headset and stem too.
Added a rear rack, stainless bottle cages, a computer and a bell.
Had fenders for a while... then I realized I don't ride in the rain anyway.
Had lights for a while... then I realized I don't rids after dark anyway.
I would replace the seat post, but I just tightened it enough that I have locked it and it is effectively no longer a suspension seat post. If I run into one to use, I may replace it to save a few grams.
I also had clipless pedals for a while, but for the type of riding I typically do on this bike, I went back to the stock pedals.
I am seriously considering a move to a Nashbar trekking bar and rapid fire shifters. I have both.
I will possibly switch to Schwalbe Big Apple tires when my current set needs replacing. I have modified my desire for speed and want to see if I like high volume slicks. I have a few drop bar bikes if I want to ride faster.