Here is a list of commands categorised according to basic function one needs to perform.

Documentation

apropos, info, locate, man, makewhatis, manpath, updatedb, whatis, whereis.

Files

chgrp,chmod,chown,cksum,cp,dd,file,install,Ln,ls,lsattr,mv,pathchk,rm,stst,sum,symlinks,touch

Process

&,^Z,bg,fg,fuser,jobs,kill,killall,nice,nohup,pidof,ps,pstree,renice,top

Standard Input,Output and Error

>,<,2>,>>,|,tee,script,xargs

Directories

cd,mkdir,pwd,rmdir,symlinks

Users

chfn,chpasswd,finger,groupmod,grpck,id,passwd,pwck,su,useradd,useradd,usermod,users,who

Paths

basename,dirname,namei,pathchk

BASH Shell

Invoking bash, Startup Files, Aliases, Command History,Command completion, command line editing, word designators, Shell variables, Shell prompts, Shell arithmetic, Looping statement, conditional statement, shell functions, Builtins

Terminal & Keyboard

captoinfo, clear, dumpkeys, getkeycodes, getty,infocmp,loadkeys,login,setterm,stty,tic,tput,tset

Disks

badblocks,cfdisk,du,fdformat,fdisk,quota,setfdprm

File Systems

debugfs,df,dumpe2fs,e2fsck,fsck,fsck.minix,fuser,lsattr,lsof,mke2fs,mkfs,mkfs.minix,mklost+found,mkswap,mount,rdev,swapoff,swapon,sync,tunee2fs,umount

Printers & Print Queues

lpc,lpd,lpq,lpr,lprm,pr,tunelp

Daemons

fingerd,ftpd,gated,gdc,identd,imapd,inetd,klogd,lpd,mountd,named,pppd,rexecd,rlogind,rcmd,rshd,rwhod,syslogd,talkd,tcpd,telnetd,tftpd,yppasswdd

Machine Information

arch,hostname,hwclock,uname

Kernel

depmod,modprobe,insmod,kerneld,ksyms,lsmod,bdflush,rmmod

Displaying Files

cat,head,less,look,rev,tac,tail

Comparing & Merging Files

comm,cmp,diff,diff3,sdiff

Data Files

columncolrm,csplit,cut,expand,fmt,fold,merge,paste,sort,split,tr,unexpand,uniq

Document Formatting

colcrt,eqn,gs,gros,gxditview,tbl,tex,troff,xdvi

VI Editor

Stopping/Starting,positing,searching,replacing,adding/deleting text, yanking/putting,Shell

Archiving & Compression

compress,cpio,dump,gzexe,gzip,gunzip,restore,shar,uncompress,uuencode,uudecode,zcmp,zdiff,zgrep,zmore,znew

Startup & Shutdown

dmesg,halt,reboot,poweroff,rdev,runlevel,shutdown,swapon,swapoff,sync,init,telinit

X-Window System

XF86Setup,X,startx,xdm,xf86config,xinit,xmseconfig,xterm,xvidtune

Scheduling

at,atq,atrm,batch,crontab,sleep,usleep

Finding Stuff

egrep,find,finger,fgrep,grep,locate,updatedb,which

Diagnostic & System Performance

df,dmesg,free,ipcs,ps,pstree,runlevel,tload,top,vmstst,who

Security

ipfwadm,pgpe,pgpk,pgps,pgpv

Miscellaneous

cal,date,fortune,ispell,rpm,strfile

TCP/IP

arp,bootpd,bootptab,bootpgw,bootptest,dip,hostname,gated,gdc,ifconfig,in.identd,netstat,nslookup,rmail,route,routed,rusers,tcpdchk,tcpdmatch,traceroute

Networking Application

ftp,hostname,netstat,ping,rarp,rcp,rdate,rdist,rlogin,rsh,rusers,rwall,rwho,telnet,tftp

NIS & NFS

domainname,nisdomainname,ypdomainname,makedbn,ypbind,ypcat,yppasswd,ypinit,yppoll,yppush,ypserv,ypset,ypwhich,ypxfer

DOS & Windows Connectivity

mattrib,mbadblocks,mcd,mdel,mdeltree,mdir,mdu,mformat,mlabel,mmd,mrd,mmove,mtype,xcopy,nmdb,smbclient,smbd,smdmount,smbstatus,smbumount,testparm

Mail & Other Communication

biff,elm,fetchmail,formail,mail,makeemap,mesg,mimencode,rmail,rwall,sendmail,talk,uuencode,wall,write