Here is the list of the programs that I use

Activator – shortcuts
OpenSSH
iCleaner Pro 7.3.0 beta from  repository http://exile90software.com/cydia/beta
FlipControlCenter – replace the original shortcut icons
IPPeek – via activator
from: https://cydia.angelxwind.net/
AppSync Unified – you need this to install unsinged ipa files.

=====TERMINALS=======

it has nice list of shortcuts, works bad on ios 9.3.3
MobileTerminal (mine bad choice)  from Karens repo https://cydia.angelxwind.net/    which is on the same code base iOS Terminal form BigBoss

MTerminal works good –  from the BigBoss repo.

http://repo.thireus.com – install recommended ios9/ios8/ios7 hacker tools, this includes “newterm” which is updated through ios9. The hacker package installs a bunch of command line utilities like ping, nmap, get, top wget, etc as well. otherwise if you just want terminal just install newterm.

=============================

AudioRecored2 from http://limneos.net/repo or

AppCake – from http://cydia.iphonecake.com/

Bridge – import music to Music from http://canolli.yourepo.com/

Tried but not using
https://appaddict.org/ios-app/ – trying now
https://www.yourepo.com/repo/canolli/pack/bridge – tring now and want to try those also
killbackground8
vShare
iFile – from here http://www.sinfuliphonerepo.com/

Not working
PasswordPilot – inserts your apple password automatically
LocallApStore from http://system.in-appstore.com/repo

Want to try

http://www.xmodgames.com/

Winterboard, Dreamboard

Nice liste of more apps http://www.islamadel.com/en/notes/8-iphone/14-iphone-apps-and-settings

Under linux I use this command to install ipa files.
ideviceinstaller -i /home/guda/Documents/iphone/ipa/openmaps.ipa
This comes from http://www.libimobiledevice.org/

You have to enable to access to your filesystem, maybe apt-get re-install fuse
here here here