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[müzso <bit2@xxxxxxxxxxx>]

This is not a launcher or Unity bug. And it's still relevant for the latest Ubuntu version (13.04).
Take a look at the *.desktop file of jEdit (it's a text editor written in Java and ships in Ubuntu's universal repository).

First of all: create a copy of jedit.desktop and modify all the relevant entries. Most of them are relevant. :-)
Now the problematic entry is StartupWMClass. If you don't set up this correctly, Unity won't be able to "identify" the process/window that is launched by the executable specified by the "Exec" entry.
You can start up SQuirreL and use xprop to get the correct value. I'll help you: it's "net-sourceforge-squirrel_sql-client-Main"

So a proper squirrel.desktop file looks like this:

[Desktop Entry]
Name=SQuirreL
GenericName=SQuirreL SQL Client
Comment=Browse/edit SQL databases
Exec=/opt/SQuirreLSQLClient/squirrel-sql.sh %U
Icon=/opt/SQuirreLSQLClient/icons/acorn.png
Terminal=false
Type=Application
Categories=Development;
StartupNotify=true
MimeType=text/x-sql;
StartupWMClass=net-sourceforge-squirrel_sql-client-Main
Keywords=Programming;Java;SQL

(Of course assuming that SquirreL is install in /opt/SQuirreLSQLClient)

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https://bugs.launchpad.net/bugs/878113

Title:
  Custom launcher for SQuirreL starts new process on every click

Status in BAMF Application Matching Framework:
  Expired
Status in Unity:
  Expired
Status in “bamf” package in Ubuntu:
  Expired
Status in “unity” package in Ubuntu:
  Expired

Bug description:
  I've managed to create a custom launcher for Squirrel (the widely-used
  SQL client, not the mail client), but whenever I click on it, it
  launches a new process. When I have already started Squirrel, clicking
  on the launcher should show the running instance, not start a new one.
  Also, as the running program is not visible in the desktop wall, I
  cannot actually resume using the running program, or even stop it
  (apart from killing the process).

  Also, I would like to modify the launcher myself, but it is not in
  ~/.local/share/applications which is where I expected it to be.

  ProblemType: Bug
  DistroRelease: Ubuntu 11.10
  Package: unity 4.22.0-0ubuntu3
  ProcVersionSignature: Ubuntu 3.0.0-12.20-generic-pae 3.0.4
  Uname: Linux 3.0.0-12-generic-pae i686
  NonfreeKernelModules: nvidia
  .proc.driver.nvidia.gpus.0: Error: [Errno 21] Is a directory: '/proc/driver/nvidia/gpus/0'
  .proc.driver.nvidia.registry: Binary: ""
  .proc.driver.nvidia.version:
   NVRM version: NVIDIA UNIX x86 Kernel Module  280.13  Wed Jul 27 16:55:43 PDT 2011
   GCC version:  gcc version 4.6.1 (Ubuntu/Linaro 4.6.1-9ubuntu3)
  .tmp.unity.support.test.0:
   
  ApportVersion: 1.23-0ubuntu3
  Architecture: i386
  CompizPlugins: [core,bailer,detection,composite,opengl,compiztoolbox,decor,grid,mousepoll,regex,animation,gnomecompat,place,vpswitch,snap,move,imgpng,session,resize,wall,workarounds,expo,unitymtgrabhandles,fade,scale,unityshell]
  CompositorRunning: compiz
  Date: Wed Oct 19 12:34:37 2011
  DistUpgraded: Log time: 2011-10-17 10:34:40.092303
  DistroCodename: oneiric
  DistroVariant: ubuntu
  DkmsStatus: nvidia-current, 280.13, 3.0.0-12-generic-pae, i686: installed
  EcryptfsInUse: Yes
  GraphicsCard:
   nVidia Corporation G84 [Quadro FX 570] [10de:040e] (rev a1) (prog-if 00 [VGA controller])
     Subsystem: nVidia Corporation Device [10de:0474]
  InstallationMedia: Ubuntu 10.10 "Maverick Meerkat" - Release i386 (20101007)
  JockeyStatus:
   xorg:nvidia_173 - NVIDIA accelerated graphics driver (Proprietary, Disabled, Not in use)
   xorg:nvidia_173_updates - NVIDIA accelerated graphics driver (post-release updates) (Proprietary, Disabled, Not in use)
   xorg:nvidia_current - NVIDIA accelerated graphics driver (Proprietary, Enabled, In use)
   xorg:nvidia_current_updates - NVIDIA accelerated graphics driver (post-release updates) (Proprietary, Disabled, Not in use)
  MachineType: Dell Inc. OptiPlex GX620
  ProcEnviron:
   LC_COLLATE=C
   PATH=(custom, user)
   LANG=en_GB.UTF-8
   SHELL=/bin/bash
  ProcKernelCmdLine: BOOT_IMAGE=/boot/vmlinuz-3.0.0-12-generic-pae root=UUID=f30b0ad9-b31f-4040-8895-24b4de430453 ro quiet splash vt.handoff=7
  SourcePackage: unity
  UpgradeStatus: Upgraded to oneiric on 2011-10-17 (1 days ago)
  dmi.bios.date: 02/20/2006
  dmi.bios.vendor: Dell Inc.
  dmi.bios.version: A06
  dmi.board.name: 0HH807
  dmi.board.vendor: Dell Inc.
  dmi.chassis.type: 6
  dmi.chassis.vendor: Dell Inc.
  dmi.modalias: dmi:bvnDellInc.:bvrA06:bd02/20/2006:svnDellInc.:pnOptiPlexGX620:pvr:rvnDellInc.:rn0HH807:rvr:cvnDellInc.:ct6:cvr:
  dmi.product.name: OptiPlex GX620
  dmi.sys.vendor: Dell Inc.
  version.compiz: compiz 1:0.9.6+bzr20110929-0ubuntu5
  version.libdrm2: libdrm2 2.4.26-1ubuntu1
  version.libgl1-mesa-dri: libgl1-mesa-dri 7.11-0ubuntu3
  version.libgl1-mesa-dri-experimental: libgl1-mesa-dri-experimental N/A
  version.libgl1-mesa-glx: libgl1-mesa-glx 7.11-0ubuntu3
  version.nvidia-graphics-drivers: nvidia-graphics-drivers N/A
  version.xserver-xorg: xserver-xorg 1:7.6+7ubuntu7
  version.xserver-xorg-input-evdev: xserver-xorg-input-evdev 1:2.6.0-1ubuntu13
  version.xserver-xorg-video-ati: xserver-xorg-video-ati 1:6.14.99~git20110811.g93fc084-0ubuntu1
  version.xserver-xorg-video-intel: xserver-xorg-video-intel 2:2.15.901-1ubuntu2
  version.xserver-xorg-video-nouveau: xserver-xorg-video-nouveau 1:0.0.16+git20110411+8378443-1

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