How do I identify remote server os and apps using UNIX or Linux command line options?

You can use the nmap command under UNIX, OS X, BSD or Linux operating systems to detect remote operating systems and running apps. Type the following command
# nmap -O -v localhost
# nmap -O -v server.ip.address
Sample outputs:

Starting Nmap 5.00 ( http://nmap.org ) at 2010-06-11 04:18 IST
NSE: Loaded 0 scripts for scanning.
Warning: Hostname localhost resolves to 2 IPs. Using 127.0.0.1.
Initiating SYN Stealth Scan at 04:18
Scanning localhost (127.0.0.1) [1000 ports]
Discovered open port 80/tcp on 127.0.0.1
Discovered open port 3306/tcp on 127.0.0.1
Discovered open port 631/tcp on 127.0.0.1
Completed SYN Stealth Scan at 04:18, 0.09s elapsed (1000 total ports)
Initiating OS detection (try #1) against localhost (127.0.0.1)
Retrying OS detection (try #2) against localhost (127.0.0.1)
Retrying OS detection (try #3) against localhost (127.0.0.1)
Retrying OS detection (try #4) against localhost (127.0.0.1)
Retrying OS detection (try #5) against localhost (127.0.0.1)
Host localhost (127.0.0.1) is up (0.000026s latency).
Interesting ports on localhost (127.0.0.1):
Not shown: 997 closed ports
PORT     STATE SERVICE
80/tcp   open  http
631/tcp  open  ipp
3306/tcp open  mysql
No exact OS matches for host (If you know what OS is running on it, see http://nmap.org/submit/ ).
TCP/IP fingerprint:
OS:SCAN(V=5.00%D=6/11%OT=80%CT=1%CU=30822%PV=N%DS=0%G=Y%TM=4C116BC7%P=i686-
OS:pc-linux-gnu)SEQ(SP=C9%GCD=1%ISR=CF%TI=Z%CI=Z%II=I%TS=8)OPS(O1=M400CST11
OS:NW6%O2=M400CST11NW6%O3=M400CNNT11NW6%O4=M400CST11NW6%O5=M400CST11NW6%O6=
OS:M400CST11)WIN(W1=8000%W2=8000%W3=8000%W4=8000%W5=8000%W6=8000)ECN(R=Y%DF
OS:=Y%T=40%W=8018%O=M400CNNSNW6%CC=Y%Q=)T1(R=Y%DF=Y%T=40%S=O%A=S+%F=AS%RD=0
OS:%Q=)T2(R=N)T3(R=Y%DF=Y%T=40%W=8000%S=O%A=S+%F=AS%O=M400CST11NW6%RD=0%Q=)
OS:T4(R=Y%DF=Y%T=40%W=0%S=A%A=Z%F=R%O=%RD=0%Q=)T5(R=Y%DF=Y%T=40%W=0%S=Z%A=S
OS:+%F=AR%O=%RD=0%Q=)T6(R=Y%DF=Y%T=40%W=0%S=A%A=Z%F=R%O=%RD=0%Q=)T7(R=Y%DF=
OS:Y%T=40%W=0%S=Z%A=S+%F=AR%O=%RD=0%Q=)U1(R=Y%DF=N%T=40%IPL=164%UN=0%RIPL=G
OS:%RID=G%RIPCK=G%RUCK=G%RUD=G)IE(R=Y%DFI=N%T=40%CD=S)

Uptime guess: 0.527 days (since Thu Jun 10 15:39:23 2010)
Network Distance: 0 hops
TCP Sequence Prediction: Difficulty=201 (Good luck!)
IP ID Sequence Generation: All zeros

Read data files from: /usr/share/nmap
OS detection performed. Please report any incorrect results at http://nmap.org/submit/ .
Nmap done: 1 IP address (1 host up) scanned in 12.11 seconds
           Raw packets sent: 1095 (51.990KB) | Rcvd: 2208 (98.632KB)