The order in most "official" checklists follow taxonomic order
as defined by the American Ornitological Union and, generally,
put the more ancient lineages ahead of the more recently evolved
(I prefer ancient to primative, because primitive carries connota-
tional baggage implying inferiority).

Until recently, North American lists started with loons (African
lists start with Ostriches), but recent fossil and genetic distance
mapping suggest ducks should come first and most new checklist
and field guides reflect this change. Expect more changes in the
future, that's what taxonomists do.

Not all field guides are laid out taxonomically. I've seen field
guides laid out by plumage color, habitat type, birds that look
kinda the same, birds that are more common to less common and lay-
outs that can only be described as "author's choice".

And Ive seen checklists laid out alphabetically in all sorts of
including:

House sparrow
House Wren
Song Sparrow

Sparrow, House
Sprarrow, Song
Wren, House

Melospiza melodia
Passer domesticus
Troglodytes aedon

I don't recommend alphabetical order for checklists...

--
Mike Patterson
Astoria, OR
celata at pacifier.com

Malheur NWR Photo Essay
http://www.surfbirds.com/blogs/mbalame/archives/2007/05/malheur200705.html