It depends on how much code you want to write yourself ...
HandDBase is very nice for flat-file databases, but has some limitations, as you note.
A free database program you could use to write a calorie lookup and logging applications is Grandasoft XForms:
http://www.grandasoft.com/
It allows a more flexible design than HandDBase. However, it does not seem to have a graph tool for forms.
Basic4ppc (
www.basic4ppc.com) is a more generalized development package. It's not free, but not too expensive. It does not have true graphics primitives, but if you look at some of the sample applications, people have been very clever in getting it to draw pictures. I'm sure you could come up with a crude bargraph with the form elements easily (see Tower of Hanoi example).
I downloaded Embedded Visual Basic 3.0 from Microsoft for free. It has a Picturebox control which allows for circle and line drawing that can be used for graphing. There are numerous ways to store tabular data, but you'd have to make your own export routines (not a big deal). It's a little more of a commitment, but it would get the job done.
Have you thought about a hybrid approach? HandDBase for recording glucose readings and a graphic calculator to show trends?
(by the way, have you seen the program by John Misurda that downloads from AccuCheck macines via IR to the Axim?
http://www.cs.pitt.edu/~jmisurda/ppc.../GlucoComm.htm)
Now that I think about it, John Misurda has been very responsive to requests for useful software. He has a blog / web page; you might want to contact him directly to see if he'll give you the source code as a place to start, or more likely he'll just add functionality himself.