Cleaning up ubuntu

Ubuntu and other flavors of Linux don't really need cleaning up as you might do in Windows. Over time, of course, you might accumulate things on your computer that you might not wish to keep - old documents, no-longer-used programs, etc. - but there is nothing really akin to the Windows registry that simply builds up clutter that slows your computer. The old stuff you save won't slow down your computer: it will probably run as fast a year from now as it does today.
To clean some packages laying around
Run:

sudo apt-get autoremove
sudo apt-get clean
sudo apt-get autoclean 

But you can do the following to clean up your computer:
Installing ubuntu tweak:

sudo add-apt-repository ppa:tualatrix/next  
sudo apt-get update  
sudo apt-get install ubuntu-tweak

and then run ubuntu-tweak and there is an option called Janitor which is used for cleaning as seen in the picture:

BLEACHBIT:

 

BleachBit  deletes unnecessary files to free valuable disk space, maintain privacy, and remove junk. Rid your system of old clutter including
       cache,  temporary files, cookies, and broken shortcuts.  It wipes clean
       Bash, Beagle, Epiphany,  Firefox,  Flash,  Java,  KDE,  OpenOffice.org,
       Opera, RealPlayer, rpmbuild, VIM, XChat, and more.

Features

BleachBit has many useful features designed to help you easily clean your computer to free space and maintain privacy.

• Simple operation: read the descriptions, check the boxes you want, click preview, and click delete.
• Multi-platform: Linux and Windows
• Free of charge
• Free to share, learn, and modify (open source)
• No adware, spyware, malware, or browser toolbars
• Translated to 60 languages
• Shred files to hide their contents and prevent data recovery
• Shred any file (such as a spreadsheet on your desktop)
• Overwrite free disk space to hide previously deleted files
• Portable app for Windows: run without installation
• Command line interface for scripting and automation
• CleanerML allows anyone to write a new cleaner using XML
• Automatically import and update winapp2.ini cleaner files (a separate download) giving Windows users access to 1200+ additional cleaners
• Frequent software updates with new features

Advanced cleaners

Going beyond standard deletion of files, BleachBit has several advanced cleaners:

• Clear the memory and swap on Linux
• Delete broken shortcuts on Linux
• Delete the Firefox URL history without deleting the whole file—with optional shredding
• Delete Linux localizations: delete languages you don't use. More powerful than localepurge and available on more Linux distributions.
• Clean APT for Debian, Ubuntu, Kubuntu, Xubuntu, and Linux Mint
• Find widely-scattered junk such as Thumbs.db and .DS_Store files.
• Execute yum clean for CentOS, Fedora, and Red Hat to remove cached package data
• Delete Windows registry keys—often where MRU (most recently used) lists are stored
• Delete the OpenOffice.org recent documents list without deleting the whole Common.xcu file
• Overwrite free disk space to hide previously files
• Vacuum Firefox, Google Chrome, Liferea, Thunderbird, and Yum databases: shrink files without removing data to save space and improve speed
• Surgically remove private information from .ini and JSON configuration files without deleting the whole file

You can install it from the software-center or by typing the following in a terminal:
sudo apt-get install bleachbit