1. Java Heap Size
Place to store objects created by your Java application, this is where Garbage Collection takes place, the memory used by your Java application. For a heavy Java process, insufficient Heap size will cause the popularjava.lang.OutOfMemoryError: Java heap space.

-Xms<size> - Set initial Java heap size
-Xmx<size> - Set maximum Java heap size

2. Perm Gen Size
Place to store your loaded class definition and metadata. If a large code-base project is loaded, the insufficient Perm Gen size will cause the popular Java.Lang.OutOfMemoryError: PermGen.

-XX:PermSize<size> - Set initial PermGen Size.
-XX:MaxPermSize<size> - Set the maximum PermGen Size.

3. Java Stack Size
Size of a Java thread. If a project has a lot of threads processing, try reduce this stack size to avoid running out of memory.
-Xss = set java thread stack size

$ java -Xss512k JavaApp

Note
The default value for heap size, perm gen, or stack size is differ from different JVMs. The best practice is always defining your own value.

2. Ubuntu

This is the testing environment :

OS  : Ubuntu 13 (64 bits) (Under VirtualBox)RAM : 4G
CPU : 1 x Processors
JDK : 1.7.0_51

$ java -XX:+PrintFlagsFinal -version | grep -iE 'HeapSize|PermSize|ThreadStackSize' 
    uintx InitialHeapSize                          := 64781184        {product}   
    uintx MaxHeapSize                              := 1038090240      {product} 
    uintx PermSize                                  = 21757952        {pd product}
    uintx MaxPermSize                               = 174063616       {pd product}
     intx ThreadStackSize                           = 1024            {pd product}          java version "1.7.0_51"OpenJDK Runtime Environment (IcedTea 2.4.4) (7u51-2.4.4-0ubuntu0.13.10.1)OpenJDK 64-Bit Server VM (build 24.45-b08, mixed mode)

In above environment, JVM allocated following default values :

1. Java heap size
   InitialHeapSize = 64781184 bytes (61.7M) and MaxHeapSize = 1038090240 bytes (990M).

2. PermGen Size
   PermSize = 21757952 bytes (20.75M), MaxPermSize = 174063616 bytes (166M)

3. Thread Stack Size
   ThreadStackSize = 1024 kilobytes (1M)

The allocated heap memory size is quite close to the ergonomics result.

#ergonomics algorithm 
Initial heap size = 4096M/64 = 64M
Maximum heap size = 4096M/4 = 1024M

3. Mac OSX

This is the testing environment :

OS  : Mac OSX 10.9RAM : 8G
CPU : 4 x Processors
JDK : 1.7.0_05

$ java -XX:+PrintFlagsFinal -version | grep -iE 'heapsize|permsize|threadstacksize' 
    uintx InitialHeapSize                          := 20655360        {product}
    uintx MaxHeapSize                              := 331350016       {product}
    uintx PermSize                                  = 21757952        {pd product}
    uintx MaxPermSize                               = 85983232        {pd product}
     intx ThreadStackSize                           = 1024            {pd product}java version "1.7.0_05"Java(TM) SE Runtime Environment (build 1.7.0_05-b05)Java HotSpot(TM) 64-Bit Server VM (build 23.1-b03, mixed mode)

1. Java heap size
   InitialHeapSize = 20655360 bytes (19.69M) and MaxHeapSize = 331350016 bytes (316M).

2. PermGen Size
   PermSize = 21757952 bytes (20.75M), MaxPermSize = 85983232 bytes (82M).

3. Java Stack Size
   ThreadStackSize = 1024 kilobytes (1M)

The allocated heap memory size is totally irrelevant if compare to the following ergonomics result.

#ergonomics algorithm 
Initial heap size = 8192M/64 = 128M
Maximum heap size = 8192M/4 = 2048M

4. Windows

There is no grep in Windows, instead, we use findstr.

This is the testing environment :

OS  : Windows 8RAM : 16G
CPU : 8 x Processors
JDK : 1.7.0_40

C:\>java -XX:+PrintFlagsFinal -version | findstr /i "HeapSize PermSize ThreadStackSize" 
    uintx InitialHeapSize                          := 266634176       {product}
    uintx MaxHeapSize                              := 4267704320      {product}
    uintx PermSize                                  = 21757952        {pd product}
    uintx MaxPermSize                               = 85983232        {pd product}
     intx ThreadStackSize                           = 0               {pd product}java version "1.7.0_40"Java(TM) SE Runtime Environment (build 1.7.0_40-b43)Java HotSpot(TM) 64-Bit Server VM (build 24.0-b56, mixed mode)

1. Java heap size
   InitialHeapSize = 266634176 bytes (256M) and MaxHeapSize = 4266146816 bytes (4068M).

2. PermGen Size
   PermSize = 21757952 bytes (20.75M), MaxPermSize = 85983232 bytes (823. M).

3. Java Stack Size
   ThreadStackSize = 0 kilobytes. (weird…)

The allocated heap memory size is almost same with the ergonomics result :

#ergonomics algorithm
Initial heap size = 16384/64 = 256M
Maximum heap size = 16384/4 = 4096M

5. Suggested Java Memory

Below is my suggested value for a small to medium Java application :)

1. Heap = -Xms512m -Xmx1024m

2. PermGen = -XX:PermSize=64m -XX:MaxPermSize=128m

3. Thread = -Xss512k

P.S For most Java projects, 512k for a thread is sufficient.

$ java -XX:+PrintFlagsFinal -Xms512m -Xmx1024m -Xss512k -XX:PermSize=64m -XX:MaxPermSize=128m    -version | grep -iE 'HeapSize|PermSize|ThreadStackSize' 
    uintx InitialHeapSize                          := 536870912       {product}
    uintx MaxHeapSize                              := 1073741824      {product}
    uintx PermSize                                 := 67108864        {pd product}  
    uintx MaxPermSize                              := 134217728       {pd product}  
     intx ThreadStackSize                          := 512             {pd product}