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At the very least, both utils and extras should be split out into more highly-targeted units and eventually dissolved.

Possibilities for smaller units into which many procedures already fit reasonably well:

format
format, printf, fprintf, ...
read
read-byte, ...
write
write-byte, ...
runtime
chicken-home, c-runtime, enable-warnings, features, gc, repository-path, ...
bench
memory
string

It might also be good to organize things hierarchically, in R7RS library style. Other Schemes do this to a greater or lesser degree, and it works well to differentiate built-ins from libraries. Also valuable would be to namespace, or at least alias, built-in units under (chicken ...).

(chicken data alist)
alist-ref, alist-update, ...
(chicken data ...)
...
(chicken i/o read)
...
(chicken i/o write)
...

The following is a dump of the non-SRFI units as they currently exist. Annotate with ideas for new locations as you see fit.

data-structures
->string
string
alist-ref
alist
alist-update
alist
alist-update!
alist
any?
atom?
binary-search
butlast
chop
complement
compose
compress
conc
string
conjoin
constantly
disjoin
each
flatten
flip
identity
intersperse
join
list->queue
queue
list-of?
make-queue
queue
merge
merge!
o
queue->list
queue
queue-add!
queue
queue-empty?
queue
queue-first
queue
queue-last
queue
queue-length
queue
queue-push-back!
queue
queue-push-back-list!
queue
queue-remove!
queue
queue?
queue
random-seed
random
rassoc
reverse-string-append
string
sort
sort!
sorted?
string-chomp
string
string-chop
string
string-compare3
string
string-compare3-ci
string
string-intersperse
string
string-split
string
string-translate
string
string-translate*
string
substring-ci=?
string
substring-index
string
substring-index-ci
string
substring=?
string
tail?
topological-sort

eval
chicken-home
runtime
eval
extension-information
load
load-library
load-noisily
load-relative
provide
provided?
repl
repository-path
runtime
require
set-dynamic-load-mode!

expand
er-macro-transformer
expand
get-line-number
ir-macro-transformer
syntax-error

extras
format
io, format
fprintf
io, format
pp
io, data
pretty-print
io, data
pretty-print-width
io, data
printf
io, format
random
random
randomize
random
read-byte
io, read
read-file
io, read
read-line
io, read
read-lines
io, read
read-string
io, read
read-string!
io, read
read-token
io, read
sprintf
io, format
write-byte
io, write
write-line
io, write
write-string
io, write

files
absolute-pathname?
path
create-temporary-directory
file
create-temporary-file
file
decompose-directory
path
decompose-pathname
path
delete-file*
file
directory-null?
file-copy
file
file-move
file
make-absolute-pathname
path
make-pathname
path
normalize-pathname
path
pathname-directory
path
pathname-extension
path
pathname-file
path
pathname-replace-directory
path
pathname-replace-extension
path
pathname-replace-file
path
pathname-strip-directory
path
pathname-strip-extension
path

library
add1
argv
arithmetic-shift
bit-set?
bitwise-and
bitwise-ior
bitwise-not
bitwise-xor
blob->string
blob-size
blob=?
blob?
build-platform
runtime
c-runtime
runtime
call/cc
char-name
chicken-version
runtime
continuation-capture
continuation-graft
continuation-return
continuation?
copy-read-table
read-syntax
cpu-time
bench
current-error-port
current-gc-milliseconds
time
current-milliseconds
time
current-output-port
current-seconds
time
define-reader-ctor
read-syntax
delete-file
file
directory-exists?
enable-warnings
runtime
equal=?
errno
error
exit
process, system
feature?
runtime
features
runtime
file-exists?
file
finite?
fixnum-bits
runtime, limits
fixnum-precision
runtime, limits
fixnum?
flonum-decimal-precision
flonum-epsilon
flonum-maximum-decimal-exponent
flonum-maximum-exponent
flonum-minimum-decimal-exponent
flonum-minimum-exponent
flonum-precision
flonum-radix
flonum?
flush-output
io, port
foldl
foldr
fp*
fp+
fp-
fp/
fp<
fp<=
fp=
fp>
fp>=
fpabs
fpacos
fpasin
fpatan
fpatan2
fpceiling
fpcos
fpexp
fpexpt
fpfloor
fpinteger?
fplog
fpmax
fpmin
fpneg
fpround
fpsin
fpsqrt
fptan
fptruncate
fx*
fx+
fx-
fx/
fx<
fx<=
fx=
fx>
fx>=
fxand
fxeven?
fxior
fxmax
fxmin
fxmod
fxneg
fxnot
fxodd?
fxshl
fxshr
fxxor
gc
runtime
gensym
get
get-call-chain
get-environment-variable
process, env
get-keyword
get-output-string
port
get-properties
getenv
process, env
getter-with-setter
keyword->string
keyword?
machine-byte-order
runtime
machine-type
runtime
make-blob
memory
maximum-flonum
runtime, limits
memory-statistics
runtime, stats
minimum-flonum
runtime, limits
most-negative-fixnum
runtime, limits
most-positive-fixnum
runtime, limits
on-exit
process, event
open-input-string
io, port
open-output-string
io, port
port-closed?
port
port-name
port
port-position
port
port?
port
print
io, write
print*
io, write
print-call-chain
print-error-message
procedure-information
promise?
put!
quit
process
register-feature!
runtime
remprop!
rename-file
file
reset
event
reverse-list->string
set-finalizer!
set-gc-report!
runtime
set-parameterized-read-syntax!
read-syntax
set-port-name!
set-read-syntax!
read-syntax
set-sharp-read-syntax!
read-syntax
setter
signum
software-type
runtime
software-version
runtime
string->blob
string->keyword
string->uninterned-symbol
sub1
subvector
symbol-append
symbol-plist
system
process, system
unregister-feature!
runtime
vector-copy!
vector-resize
void
warning

lolevel
address->pointer
align-to-word
allocate
memory
block-ref
block-set!
extend-procedure
extended-procedure?
free
memory
locative->object
locative-ref
locative-set!
locative?
make-locative
make-pointer-vector
make-record-instance
make-weak-locative
move-memory!
memory
mutate-procedure!
number-of-bytes
number-of-slots
object->pointer
object-become!
object-copy
object-evict
object-evict-to-location
object-evicted?
object-release
object-size
object-unevict
pointer+
pointer->address
pointer->object
pointer-f32-ref
pointer-f32-set!
pointer-f64-ref
pointer-f64-set!
pointer-like?
pointer-s16-ref
pointer-s16-set!
pointer-s32-ref
pointer-s32-set!
pointer-s8-ref
pointer-s8-set!
pointer-tag
pointer-u16-ref
pointer-u16-set!
pointer-u32-ref
pointer-u32-set!
pointer-u8-ref
pointer-u8-set!
pointer-vector
pointer-vector-ref
pointer-vector-set!
pointer-vector?
pointer=?
pointer?
procedure-data
record->vector
record-instance-length
record-instance-slot
record-instance-slot-set!
record-instance-type
record-instance?
set!
set-procedure-data!
tag-pointer
tagged-pointer?
vector-like?

ports

This unit is already pretty sane.

call-with-input-string
port
call-with-output-string
port
copy-port
port
make-broadcast-port
port
make-concatenated-port
port
make-input-port
port
make-output-port
port
port-fold
port
port-for-each
port
port-map
port
with-error-output-to-port
port
with-input-from-port
port
with-input-from-string
port
with-output-to-port
port
with-output-to-string
port

posix
_exit
process, system
block-device?
file
call-with-input-pipe
io, port
call-with-output-pipe
io, port
change-directory
change-directory*
change-file-mode
file
change-file-owner
file
character-device?
file
close-input-pipe
io, port
close-output-pipe
io, port
create-directory
create-fifo
file
create-pipe
io, fd
create-session
process
create-symbolic-link
current-directory
process
current-effective-group-id
process
current-effective-user-id
process
current-group-id
process
current-process-id
process
current-user-id
process
delete-directory
directory
directory?
duplicate-fileno
fd
errno/acces
errno/again
errno/badf
errno/busy
errno/child
errno/exist
errno/fault
errno/intr
errno/inval
errno/io
errno/isdir
errno/mfile
errno/noent
errno/noexec
errno/nomem
errno/nospc
errno/notdir
errno/perm
errno/pipe
errno/rofs
errno/spipe
errno/srch
errno/wouldblock
fcntl/dupfd
fd, file
fcntl/getfd
fd, file
fcntl/getfl
fd, file
fcntl/setfd
fd, file
fcntl/setfl
fd, file
fifo?
file
file-access-time
file
file-change-time
file
file-close
file
file-control
file
file-creation-mode
file
file-execute-access?
file
file-link
file
file-lock
file
file-lock/blocking
file
file-mkstemp
file
file-modification-time
file
file-open
file
file-owner
file
file-permissions
file
file-position
file
file-read
file
file-read-access?
file
file-select
file
file-size
file
file-stat
file
file-test-lock
file
file-truncate
file
file-type
file
file-unlock
file
file-write
file
file-write-access?
file
fileno/stderr
io, fd
fileno/stdin
io, fd
fileno/stdout
io, fd
find-files
get-environment-variables
process, env
get-groups
process
get-host-name
process, system
glob
group-information
process
initialize-groups
system
local-time->seconds
time
local-timezone-abbreviation
time
map-file-to-memory
memory
memory-mapped-file-pointer
memory
memory-mapped-file?
memory
open-input-file*
io, fd
open-input-pipe
io
open-output-file*
io, fd
open-output-pipe
io
open/append
open/binary
open/creat
open/excl
open/fsync
open/noctty
open/nonblock
open/rdonly
open/rdwr
open/read
open/sync
open/text
open/trunc
open/write
open/wronly
parent-process-id
process
perm/irgrp
perm/iroth
perm/irusr
perm/irwxg
perm/irwxo
perm/irwxu
perm/isgid
perm/isuid
perm/isvtx
perm/iwgrp
perm/iwoth
perm/iwusr
perm/ixgrp
perm/ixoth
perm/ixusr
port->fileno
io, port, fd
process
process
process*
process
process-execute
process
process-fork
process
process-group-id
process
process-run
process
process-signal
process, signal
process-spawn
process
process-wait
process
read-symbolic-link
file
regular-file?
file
seconds->local-time
time
seconds->string
time
seconds->utc-time
time
set!
set-alarm!
signal
set-buffering-mode!
port
set-file-position!
set-groups!
process
set-process-group-id!
process
set-root-directory!
process, system
set-signal-handler!
signal
set-signal-mask!
signal
setenv
process, env
signal-handler
signal
signal-mask
signal
signal-mask!
signal
signal-masked?
signal
signal-unmask!
signal
signal/abrt
signal
signal/alrm
signal
signal/chld
signal
signal/cont
signal
signal/fpe
signal
signal/hup
signal
signal/ill
signal
signal/int
signal
signal/io
signal
signal/kill
signal
signal/pipe
signal
signal/prof
signal
signal/quit
signal
signal/segv
signal
signal/stop
signal
signal/term
signal
signal/trap
signal
signal/tstp
signal
signal/urg
signal
signal/usr1
signal
signal/usr2
signal
signal/vtalrm
signal
signal/winch
signal
signal/xcpu
signal
signal/xfsz
signal
sleep
process
socket?
file
string->time
time
symbolic-link?
file
system-information
system, runtime
terminal-name
terminal-port?
terminal-size
time->string
time
unmap-file-from-memory
memory
unsetenv
process, env
user-information
system
utc-time->seconds
time
with-input-from-pipe
io, port
with-output-to-pipe
io, port

utils
compile-file
compile-file-options
qs
system
read-all
io, read
scan-input-lines
io, read
system*
system, process
yes-or-no?
system