We all know about how O. Beetle Beetle was named, and granted, that was pretty funny. However, there are lots of things about the naming of Septimus himself that I've noticed while reading and re-reading the series.
Septimus is introduced to the story (that is, after he is taken away from his family) as Boy 412. This actually went unnoticed by me until my sister pointed it out, but 4+1+2=7. Seven constantly appears in the books, and I'm sure Angie Sage had this one planned out from the start.
Later in the story, we discover that Boy 412 is Septimus Heap - the seventh son of a seventh son. This one is more obvious. "Sept" is the prefix meaning seven. Once again, Septimus' name leads back to seven.
In addition, as someone who learns Latin in school, it came to my attention that during Septimus' Darke Week, he uses the name "Sum" to avoid his true identity being revealed. He says, "Sum: I am." At this point I vaguely remember putting my book down for a minute because "sum" means "I am" in Latin.
So, basically, Septimus' name ties in a lot to certain things in the series, particularly the number seven and some Latin words.