This seems like the most sensible wad manager at the moment:

Main threads:
http://gbatemp.net/index.php?showtopic=210290&st=0&start=0
http://code.google.com/p/yawmm/

A continuation of Leathl's Wad Manager Multimod
Features added

Hold +/- for 2 seconds to select all items in a directory.
Supports Hermes v4/v5 cIOS. Mainly useful if 202 works best for your HDD/SDHC card.
More detailed failed report after batch un/installs.
Will not uninstall The System Menu, the SM's region EULA or rgsel, or their IOSs.
Will not install the wrong regions SM.
Will not load stub IOS.
Will not install titles if they rely on a stub IOS
Will not install stub SM, EULA and rgsel IOS.
Will not install SM lower than 4.0 on boot2v4 Wiis.
Gives a warning when uninstalling the HBCs IOS.
Read config file from usb.
Can load an alternative background from /wad/background.png
Won't load incompatible cIOS in SNEEK

Not a feature: I've heard some say no wad manager works with SNEEK. This one does if you don't have any incompatible cIOSs installed.

Known Issues

It will only install fakesigned wads with cIOS249x rev18 or Hermes v5 cIOSs if IOS38 is used as a base.

To do

Network update.

Items marked with * are in the testing release

Wishlist

SMB support.
?

Links

Current r19 Download http://yawmm.googlecode.com/files/boot.dolWill definitely load config/background from USB, Final brick block added (I think)
Readme http://code.google.com/p/yawmm/wiki/yawmm_ReadMe
Issues http://code.google.com/p/yawmm/issues/list
Source http://code.google.com/p/yawmm/source/checkout

Old versions http://code.google.com/p/yawmm/downloads/list?q=label:Deprecated

If you have any feature requests don't be scared to ask.

Anyone know how to get in touch with the webrewwii people please let me know