The following approach works for this type of directory tree:
$ tree .
.
├── adir1
│ ├── afile1
│ ├── afile2
│ ├── afile3
│ └── afile4.txt
├── adir2
│ ├── afile1
│ ├── afile2
│ ├── afile3
│ └── afile4.txt
├── adir3
│ ├── afile1
│ ├── afile2
│ ├── afile3
│ └── afile4.txt
├── afile1
├── afile2
├── afile3
├── foo.test
This was the solution that worked for this scenario (which I believe is the more general case).
$ find . -type f -not -path '*/\.*' -exec zip -r test.zip {} +
Example
$ find . -type f -not -path '*/\.*' -exec zip -r test.zip {} +
updating: adir1/afile1 (stored 0%)
updating: adir1/afile1.zip (stored 0%)
updating: adir1/afile2 (stored 0%)
updating: adir1/afile3 (stored 0%)
updating: adir1/afile4.txt (stored 0%)
updating: adir2/afile1 (stored 0%)
updating: adir2/afile2 (stored 0%)
updating: adir2/afile3 (stored 0%)
updating: adir2/afile4.txt (stored 0%)
updating: adir3/afile1 (stored 0%)
updating: adir3/afile2 (stored 0%)
updating: adir3/afile3 (stored 0%)
updating: adir3/afile4.txt (stored 0%)
updating: afile1 (stored 0%)
updating: afile2 (stored 0%)
updating: afile3 (stored 0%)
updating: foo.test (deflated 87%)
1Claeys - My example workerd for me, but to be fair, I used Ch Shell (includes zip) under Win7. I CDed into my test directory, and used 'zip -r test.zip ./ -x ..' (minus the single quotes). If I use 'zip -r mydir.zip mydir -x "/."' (minus the single quotes), it doesn't exclude the hidden file in my test directory. I guess it's down to differences in the shells used to test with. – Joe Internet – 2010-08-22T19:01:15.453