I use caller ID (ANI) to identify existing customers at the time we
answer the call in order bring up address/account information quickly.
In general, it is rare for one phone number to have more than one
address/account but it happens occasionally because one person might
order for several different accounts at different addresses from one
phone number.  When a new customer calls, the number that appears in
the caller ID field will be associated with the new account
information after the transaction is complete so the address/account
information will appear the next time they call.  However, in the case
of VOIP numbers, it seems like the same phone number as a rule appears
for several different unrelated addresses/accounts and the only thing
any of the businesses actually have in common is their zip code.

Is there a standard format for VOIP phone numbers that distinguishes
them from non-VOIP numbers? For example, 909 003 1041 is a VOIP
number.  Unless I'm mistaken, non-VOIP phone numbers never have a
prefix that begins with a 0.  If there isn't a standard formatting for
all VOIP numbers, is there a list somewhere or anything available that
can help me manually discern VOIP numbers from non-VOIP numbers? The
system I use to match accounts with phone numbers allows me to
manually exclude specific phone numbers from the matching process.

For example, 909 003 1041 is a VOIP number that brings up 15 different
businesses to choose from in my database.  After looking at the
businesses, the only thing they all have in common is the zip code. 
In order to prevent incorrect account selection when this number
appears, I manually excluded this phone number from allowing account
matching and it won't happen again with this one VOIP number.

I am guessing the standard would depend on the VOIP provider and there
is no standard for it. I wonder what would happen if a customer
transfers a regular number to a VOIP and keep the same number.

Just some thoughts.

Early phone switches make mechanical assumptions about what sequence of numbers
could constitute an Area Code or Exchange number.

With the explosion of phone users, some of those assumptions were
changed and newer software phone switches handle a larger variety of
Area Codes and Exchanges.
Voice over IP companies being entirely digital in their switching can can deal
with any sort of numbering system.

So, they are getting oddball exchanges you are seeing. 

http://www.thedirectory.org/pref/telfaq.htm