http://www.cyberciti.biz/tips/top-linux-monitoring-tools.html , 2012-01-03.

Main points:

#1: top - Process Activity CommandThe  top  program provides a dynamic real-time view of a running system i.e.  actual process activity. By default, it displays the most CPU-intensive tasks running on the server and updates the list every five seconds.
#2: vmstat - System Activity, Hardware and System InformationThe command vmstat reports information about processes, memory, paging, block IO, traps, and cpu activity.
#3: w - Find Out Who Is Logged on And What They Are Doingw command displays information about the users currently on the machine, and their processes.
#4: uptime - Tell How Long The System Has Been RunningThe uptime command can be used to see how long the server has been running. The current time, how long the system has been running, how many users are currently logged on, and the system load averages for the past 1, 5, and 15 minutes.
#5: ps - Displays The Processesps command will report a snapshot of the current processes. To select all processes use the -A or -e option:
#6: free - Memory UsageThe command free displays the total amount of free and used physical and swap memory in the system, as well as the buffers used by the kernel.
#7: iostat -  Average CPU Load, Disk ActivityThe command iostat report Central Processing Unit (CPU) statistics and input/output statistics for devices, partitions and network filesystems (NFS).
#8: sar - Collect and Report System ActivityThe sar command is used to collect, report, and save system activity information. To see network counter, enter:
#9: mpstat -  Multiprocessor UsageThe  mpstat  command displays activities for each available processor, processor 0 being the first one.  mpstat -P ALL to display average CPU utilization per processor:
#10: pmap - Process Memory UsageThe command pmap report memory map of a process. Use this command to find out causes of memory bottlenecks.
#11 and #12: netstat and ss -  Network StatisticsThe command netstat displays network connections, routing tables, interface statistics, masquerade connections, and multicast memberships.  ss command is used to dump socket statistics. It allows showing information similar to netstat. See the following resources about ss and netstat commands:</p><ul><li><a
#13: iptraf - Real-time Network StatisticsThe iptraf command is interactive colorful IP LAN monitor.  It is an ncurses-based IP LAN monitor that generates various network statistics including TCP info, UDP counts, ICMP and OSPF information, Ethernet load info, node stats, IP checksum errors, and others. 
#14: tcpdump - Detailed Network Traffic AnalysisThe tcpdump is simple command that dump traffic on a network. However, you need good understanding of TCP/IP protocol to utilize this tool.  For.e.g to display traffic info about DNS, enter:
#15: strace -  System CallsTrace system calls and signals. This is useful for debugging  webserver and other server problems. See how to use to <a
#16: /Proc file system - Various Kernel Statistics/proc file system provides detailed information about various hardware devices and other Linux kernel information. See <a

Then, extras from blog comments:

collectl   - perl-based, covers many aspects (disk, net, memory, cpu, ...) as interactive process or daemon logger

nmap - scan your server for open ports.
lsof - list open files, network connections and much more.
ntop - see network usage in a way similar to what top command does for processes i.e. it is network traffic monitoring software. You can see network status, protocol wise distribution of traffic for UDP, TCP, DNS, HTTP and other protocols.
vnstat - vnStat is a console-based network traffic monitor. It keeps a log of hourly, daily and monthly network traffic for the selected interface(s).
htop - htop is an enhanced version of top, the interactive process viewer, which can display the list of processes in a tree form.
mtr - mtr combines the functionality of the traceroute and ping programs in a single network diagnostic tool.

Conky - Another good monitoring tool for the X Window System. It is highly configurable and is able to monitor many system variables including the status of the CPU, memory, swap space, disk storage, temperatures, processes, network interfaces, battery power, system messages, e-mail inboxes etc.

GKrellM - It can be used to monitor the status of CPUs, main memory, hard disks, network interfaces, local and remote mailboxes, and many other things.

mrtg  multiroute traffic grapher;  nettraffic graphs

monit  utility for managing and monitoring, processes, programs, files, directories and filesystems on a UNIX system
mrtg   You have a router, you want to know what it does all day long? Then MRTG is for you..tsni

powertop  about cpu power-state and what's holding it high

justniffer   a tcp packet sniffer. It can log network traffic in a 'standard' (e.g. common webserver access.log) or in a customized way.

mystat (mysql requests)

dstat (vm,io,if,net,+)stat 

whowatch  (logged-in users /and/ their processes)

dtrace  to know more about the behavior of the operating system and its programs internals

iftop - net-interface rates sorted by process

atop   - interactive monitor to view the load on a Linux system. It shows the occupation of the most critical hardware resources (from a performance point of view) on system level, i.e. cpu, memory, disk and network.It also shows which processes are responsible for the indicated load with respect to cpu- and memory load on process level; disk- and network load is only shown per process if a kernel patch has been installed.

ethstatus - console-based monitoring utility for displaying statistical data of the ethernet interface; similar to iptraf but is meant to run as a permanent console task to monitor the network load

tcmpdump  - packet sniffing 

nload - console application which monitors network traffic and bandwidth usage in real time

traceroute - network routing discovery

monitorix -  lightweight system monitoring tool designed to monitor as many services and system resources as possible

jnettop - traffic visualiser that captures traffic going through its host and displays streams sorted by their rate

apachetop - continuously updating view of traffic based on apache webserver logs

iotop - input/output rates (showing responsible process)

vnstat - network traffic monitor 

ngrep  - network grep: PCRE matching within net packets

nmon - (local)system monitoring, similar data to 'topas', different display

bmon - graphs/tracks network activity/bandwidth real time.

swatch - track your log files and fire off alerts

etherape - great visual indicator of what traffic is going where on the network

wireshark - tcpdump on steroids.

lsdev - list of installed devices

lsmod - list of installed modules

ldd - to see dependencies of a executable file

stat - details of any file

watch - automated refresh of any code every specified seconds, etc

multitail - tail multiple files in a single terminal window



# putting these together (without duplication) and trying on an up-to-date (2012-01) Gentoo system 
# that already has my standard assortment of programs installed, the following was done, where 
# 'a' is a list of the above commands, and 'A' is the output list showing whether the command is 
# already available, or else whether a package (ebuild) of that name is available
# export PATH=$PATH:/sbin:/usr/sbin:/usr/local/sbin ; cat a | sort |  while read f ; do if which $f >/dev/null 2>&1 ; then echo "$f:  `which $f`: `equery b $(which $f) | perl -p -e 's/\s+/ /g'`"; else echo "$f: (none): `emerge -s $f | perl -p -e 's/\s+/ /g'`"; fi  ; done  | tee A
# the results (with the extra text about "checking..." and "this package does..." were: 
# NAME:  COMMAND-ALREADY-PRESENT:  OWNING-PACKAGE (or details of available package of that name)
atop: (none): sys-process/atop  (http://www.atcomputing.nl/Tools/atop) [Resource-specific view of processes]
bmon: (none): net-analyzer/bmon (http://people.suug.ch/~tgr/bmon/) [interface bandwidth monitor]
collectl: (none): sys-apps/collectl (http://collectl.sourceforge.net/) [light-weight performance monitoring tool, interactive or daemon]
dstat: (none): sys-apps/dstat  (http://dag.wieers.com/home-made/dstat/) [versatile replacement for vmstat, iostat and ifstat]
dtrace: (none): net-dialup/dtrace (ftp://ftp.avm.de/develper/d3trace/) [traces ISDN messages with AVM ISDN-controllers]
ethstatus: (none): net-analyzer/ethstatus (http://ethstatus.calle69.net/) [ncurses based utility to display real time statistics about network traffic]
iftop: (none): net-analyzer/iftop  (http://www.ex-parrot.com/~pdw/iftop/)  [display bandwidth usage on an interface]
iptraf: (none): net-analyzer/iptraf-ng (https://fedorahosted.org/iptraf-ng/) [console-based network monitoring utility, fork of iptraf 3.0.0]
jnettop: (none): net-analyzer/jnettop (http://jnettop.kubs.info/) [top-like console network traffic visualiser]
monitorix: (none): (none)
multitail: (none): app-text/multitail  (http://www.vanheusden.com/multitail/index.html) [tail with multiple windows]
mystat: (none): (none)
ngrep: (none): net-analyzer/ngrep (http://ngrep.sourceforge.net/) [grep for network layers]
nload: (none): net-analyzer/nload (http://www.roland-riegel.de/nload/index.html) [console application which monitors network traffic and bandwidth usage]
nmon: (none): sys-process/nmon (http://nmon.sourceforge.net/) [performance MONitor for CPU, memory, network, disks, etc.]
ntop: (none): net-analyzer/ntop (http://www.ntop.org/products/ntop/) [network traffic analyzer with web interface]
powertop: (none): sys-power/powertop  (http://www.lesswatts.org/projects/powertop/) [find what software is using the most power]
ss: (none): (none)
swatch: (none): app-admin/swatch  (http://swatch.sourceforge.net/) [perl-based system log watcher]
tcmpdump: (none): (none)
vnstat: (none): net-analyzer/vnstat  (http://humdi.net/vnstat/) [console-based network traffic monitor]
wireshark: (none): net-analyzer/wireshark (http://www.wireshark.org/) [network protocol analyzer formerly known as ethereal]  
apachetop:  /usr/bin/apachetop: app-admin/apachetop-0.12.6-r1 
etherape:  /usr/bin/etherape: net-analyzer/etherape-0.9.12 
free:  /usr/bin/free: sys-process/procps-3.2.8_p11 
htop:  /usr/bin/htop: sys-process/htop-0.9-r2 
iostat:  /usr/bin/iostat: app-admin/sysstat-10.0.2 
iotop:  /usr/bin/iotop: sys-process/iotop-0.4.3 
ldd:  /usr/bin/ldd: sys-libs/glibc-2.13-r4 
lsdev:  /usr/bin/lsdev: app-admin/procinfo-18-r1 
lsmod:  /bin/lsmod: sys-apps/module-init-tools-3.16-r1 
lsof:  /usr/bin/lsof: sys-process/lsof-4.83 
mpstat:  /usr/bin/mpstat: app-admin/sysstat-10.0.2 
netstat:  /bin/netstat: sys-apps/net-tools-1.60_p20110409135728 
nmap:  /usr/bin/nmap: net-analyzer/nmap-5.51 
pmap:  /usr/bin/pmap: sys-process/procps-3.2.8_p11 
ps:  /bin/ps: sys-process/procps-3.2.8_p11 
sar:  /usr/bin/sar: app-admin/sysstat-10.0.2 
stat:  /usr/bin/stat: sys-apps/coreutils-8.7 
strace:  /usr/bin/strace: dev-util/strace-4.6 
tcpdump:  /usr/sbin/tcpdump: net-analyzer/tcpdump-3.9.8-r1 
top:  /usr/bin/top: sys-process/procps-3.2.8_p11 
traceroute:  /usr/bin/traceroute: net-analyzer/traceroute-2.0.15 
uptime:  /usr/bin/uptime: sys-process/procps-3.2.8_p11 
vmstat:  /usr/bin/vmstat: sys-process/procps-3.2.8_p11 
w:  /usr/bin/w: sys-process/procps-3.2.8_p11 
watch:  /usr/bin/watch: sys-process/procps-3.2.8_p11 
whowatch:  /usr/bin/whowatch: app-admin/whowatch-1.8.3