the false positives that have been reported to me have fallen into to five
basic camps: hidden process, hidden files under /usr/lib, a specific file
is found, legitimate sniffers, and listening on well known ports.

the hidden processes problem *seems* to be a thing of the past.  mostly it
was due to the difference between how threads were reported under 2.4 and
2.6.

the hidden files issue continues to crop up now and again.  basically,
if chkrootkit sees a hidden file (a file that begins with .) under
/usr/lib, it flags it as suspicious.  there are various packages that
contain these hidden files and they are innocuous.  however, it appears
that arbitrary hidden files under /usr/lib is a sign of a rootkit, so,
again, it's the safe vs sorry argument.

the well known port issue also comes up frequently.  the problem is that
many well known ports are also used by rootkits (to get around firewalls
and as camouflage).  chkrootkit doesn't currently do any additional
checking when it finds a process listening on a port that's known to have
been used for a rootkit.

the sniffer check is just an informational check, it doesn't necessarily
mean that you've been rooted.  there are several legitimate sniffers out
there; however, you may still want to check that the sniffer is the one
that you think it is, etc.

In general, any process starting at around same time as lkm test may
trigger a warning. Just try while true;do chkrootkit lkm;sleep 1;done
during normal system use. See also FAQ 6 on www.chkrootkit.org -- paolo

chroot environments may cause "suspicious file" false positives.

bindshell listens on a lot of ports.  these ports are also used by other
legitimate programs.  chkrootkit's detection algorithm cannot determine
the difference between a legitimate program and bindshell.

below is a (non-exhaustive) list of packages that are known to cause false
positives.  before filing a bug report, please check this list.

listens on well known ports
  *radius: the Slapper worm listens on 1812
  bitlbee: LDP worms listen on port 6667
  cfs: bindshell listens on port 3049
  erlang-base: bindshell listens on port 4369
  exim-tls: bindshell listens on port 465
  mldonkey-server: bindshell listens on port 4000
  nfs-common: rpc.statd listens on port 3049
  portsentry: listens on several ports that chkrootkit sees as rootkit ports
  postfix-tls: bindshell listens on port 465
  reaim: bindshell listens on port 5190

legitimate sniffers
  dhcpd
  ethereal
  knockd
  p0f
  pppoe
  tcpdump

hidden files http://www.chkrootkit.org/faq/#8
  perl packages sometimes have .packlist files
  blackdown java
  blender
  geomview
  gnustep-make
  kaffe
  obliq
  mindi
  r-cran-hmisc
  realplay
  scilab
  smlnj
  subversion
  tiger
  twiki
  viewglob

contains specific files
  asp: Ramen Worms contain the file /usr/bin/asp
  libgcj-common: the 'OBSD rk v1' contains 
    /usr/lib/security, 
    /usr/lib/security/classpath.security 
    /usr/lib/security/libgcj.security. 
  libproc-dev: t0rn v8 contains a libproc.a
  run: ZK rootkits contain /usr/bin/run
  slice: RH-Sharpe contains /usr/bin/slice
