Software

Flexera Software 's AdminStudio is currently your best choice.

there are some other tools as well  ( cheaper, less features...less quality) 

But I cannot recommend them..

I don't use any but from what i hear admin studio is very nice. Plus there is good info at ITNINJA about admin studio if you ever need assistance. 

I don't use any I find the silent install commands to use

Personally, I prefer Wise Package Studio, but Symantec has discontinued it.

AdminStudio is kind of the 600-pound gorilla in repackaging now that Wise is gone.  It has a great enterprise feature set and a large installed base.  Symantec is actually pushing it now as a replacement to Wise.  However, we decided not to go with AdminStudio because of the price.  It was way outside our budget for packaging software.

I'm currently using Dell/Quest/ScriptLogic MSI Studio (along with Wise, until it stops working).  It's relatively inexpensive.  The vendor support, despite having jumped through a couple of buyouts, has been very good so far.  We've identified a bug or two, which they've promptly started fixing.  We've also passed on suggestions to improve it, which they've listened to (and may or may not implement).  So I wouldn't say it's a fantastic product, but it's proven to be "good enough" for us.  We were able to outfit five repackagers with it for less than the maintenance price on Wise, and for about a fourth of what Flexera wanted for AdminStudio.  (Plus, these licenses included 3 years of maintenance.)

I also looked at Caphyon Advanced Installer, which is pretty nice and can do a ton of different things.  I think it was probably my next choice after MSI Studio.  We felt like it was overkill for us, and a bit more expensive than MSI Studio... but still cheaper than AdminStudio.

EMCO MSI Package Builder wasn't bad either, but it felt very primitive and rudimentary. 

There are some others on the market as well.  I'd recommend doing some web searches to identify the different tools.  Look at screenshots and feature lists to see if what you require is part of that product.  If so, download a trial and put it through its paces.  Make sure you do as many different packages as you can during the trial period.  Try things like changing the order of custom actions, adding an active setup to a package, modifying an existing MSI, etc., in addition to capturing.  The idea is to run through a series of tests that simulate how you will actually use the product once you buy it.