I have a 'guide' that maybe can help you guys but it's a bit technical. Basically Cydia is the frontend or GUI for apt-get. You can manually install or update any package as you like.

First method might help you in refreshing the Cydia. Both method requires you to have at least Mobile Terminal installed in your phone (if got SSH lagi bagus).

1. Manually refresh Cydia
- Open Mobile Terminal and use the 'SU' command or connect to phone thru putty or terminal.
- password: alpine
- Type in "apt-get update"
- This will refresh the list from all the repo.
- Open Cydia

2. Manually installing apps from terminal or putty
- Open Mobile Terminal and use the 'SU' command or connect to phone thru putty or terminal.
- password: alpine
- Type in "apt-get install openssh" if you want to install OpenSSH

Mobile Terminal (it's a must for me) installed.

3. Upgrade the APT and Cydia Installer
- Open Mobile Terminal @ PuTTY @ Terminal
- Open Mobile Terminal and use the 'SU' command or connect to phone thru putty or terminal.
- password: alpine
- Type in "apt-get upgrade"

This is a tutorial for any of you who wants to install Cydia applications but don't have any possibility of connection to the Internet throught the iPhone/iPod Touch.

First of a list of things you will need:
- Already installed iTunes
- Cyder (software for browsing Cydia repos on PC) link
- USB cable connection (any of the devices stated above)
- Already jailbroken device with installed Cyida (of course)
- iFunBox (optional - I prefer to use it coz cyder sometime don't transfer the files correctly)

That's it

1) Install Cyder anywhere on your PC
2) Install iFunBox

3) Run Cyder (there are 4 icons on the left of the app)
4) On the first screen(icon) is a list of sources, you can add the most common ones (Clicking the + sing) (I will post a list at the end of the post).
4) After the sources are added and loaded clink the second icon
5) Here you can search for your apps. As an example we will try to install Winterboard (from a fresh jailbroekn iPhone)

6) in the search field (at the bottom) type Winterboard.
7) press the magnifying tool next to the text box to search
8) you will have to press it many times...coz it searches names, descriptions and so on...so until in the list says Winterboard keep pressing the search button.
9) once you found it (or scroll down and select it by your own) select it with the checkbox
10) notice the right part of the screen now...there is the description of the app and under it is a list of apps that needs to be installed before you can install Winterboard (in this case it says mobilesubstrate ...and some numbers)....CLICK on it to find it!!
11) once you did ...select it also with the checkbox!
12) Click the "Download selected packages" button (at the bottom-left of the page)...wait for them to download.

13) close cyder and open iFunBox
14) navigate to:
Raw File System/var/root/Media/Cydia/AutoInstall
15) if the folder Cydia/AutoInstall is not there....create it! (beware IS casesensitive)
16) the downloaded apps form cyder are in the "archives" folder where cyder is installed. They should have the DEB extension!
17) copy those files to the above indicated location!

18) Run cydia for first time reorgananization! run once more and choose "User"
19) Reboot your device by holding Home+Power 10sec
20) Don't do anything for a couple of seconds (wait untill it installs)
21) run cydia and check in the "Manage/Packages" if what you choose is installed!
22) Reboot your device once again (this is required only coz Winterboard requires it)

23)That's it...once it's booted up you should have winterboard up and running

24) There are sometimes issues of not showing the Icon on the springboard...to fix this do the following (Do it ONLY if you follwed everything and you don't get the apps icon the the springboard):
25) Download and install an app (repeating the same process from (6)) that REQUIRES the "Restart Springboard" function. For exapmle...you can install Clippy!
26) once installed go into cydia...and UNINTALL clippy (or the app of your choise) like you would normally do
27) cydia will ask you to restart the springboard - DO IT!
28) Now the icon should show up