Super Mario Bros., Super Mario Bros. 3, and Super Mario Galaxy are probably his highest shining moments.
In Super Mario Bros., not only has he managed to lay siege to the entire kingdom, but anyone that stands in his way... is silenced. Turned into a block. Or a tree. His main motivation for capturing Peach this first time is simply because he can't let her or her retainers (hi guys!!) undo his work. However, it could be said that Bowser developed feelings for her during this time. ;) Also, his castle... his castle? World 8 in general appears to be a simple mountain area, with World 8-3 at the top. Even in All-Stars, it just looks like a huge castle in the background that he took over and pasted his picture all over.
Super Mario Bros. 3 is arguably his greatest work. Introducing several large aircraft (and a few lines of ground and naval forces) and his children into the mix, Bowser seemed to be quite genius in this installment, expanding on his transformation plans from the first game and applying them to the kings of the whole Mushroom World. Plus, his castle was cooler, and actually looked like it belonged to him. Giant Bowser head outside, front yard of doom, etc.
Super Mario Galaxy: bringing back the airships, Bowser actually manages to do some serious harm in the end (it got better), and plus... he's going for a whole galaxy this time!