DOS 3.x only commands:

INIT filenameFormats disk, current BASIC program saved as boot app.
MON [,C][,I][,O]Traces DOS 3.3 commands
NOMON [,C][,I][,O]Cancels tracing of DOS 3.3 commands
MAXFILES nReserves buffers for disk i/o
FPSwitches to Applesoft BASIC, erases program in memory
INTSwitches to Integer BASIC, erases program in memory

ProDOS's BASIC.SYSTEM only commands:

CAT40-column directory listing.
PREFIX [dirname]Displays current directory or changes current dir.
CREATE filenameCreates a file with optional type
- filenameExecutes Applesoft, binary, text, system file
BYEExits to ProDOS application switcher
FLUSHWrites all buffers to disk
CHAIN filenameRuns another Applesoft program, variables intact
FREFaster Applesoft string garbage collection
STORE filenameWrites Applesoft variables to a file
RESTORE filenameReads Applesoft variables from a file
MTRJumps to monitor (same as 'CALL -151')

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Section 4: In depth explanation of commands, optional params

4.1: DOS 3.x file names and types

DOS 3.x filenames can from 1-30 characters in length, and must start
with an uppercase letter. They cannot contain commas, colons, but can
contain control characters. (Return (control-M) is a pain to type, and
thus usually out). DOS 3.x has essentially 8 filetypes, noted by the
character in the directory listing: Applesoft Basic (A), Integer Basic
(I), Text file (T), Binary (B), 'S' (source? -- rarely used) type
files, and 'R' (relocatable-- also rarely used) files, plus a second
'A' and 'B'.

A sample directory listing from a CATALOG is shown below:

DISK VOLUME 254
*A 006 HELLO
*I 018 ANIMALS
*T 003 APPLE PROMS
*B 010 BOOT13

The leftmost column contains either a '*' or is empty. A '*' means the
file is 'LOCKed' against accidental deletion or overwriting, a blank
space means that it can be saved over or deleted at will. The next
column is the filetype, as noted above. The third column, of three
digit numbers, represents the file size on disk in number of 256-byte
sectors used. [If this size is greater than 255, the number is modulo
256]. Finally, the filename is given.

4.2 ProDOS file names and types

ProDOS is far more limited in its filenames. Names are up to 15
characters, must start with a letter, and can contain letters, digits
[0..9] and the period. Filenames are essentially case insensitive,
though they are always displayed as uppercase on disk.

ProDOS also allows directories and volume names; components are
separated with the forward slash ('/') used by OSs whose designers
weren't being idiotic, like MS-DOS.