Many of the problems people have with the vApp are common issues that can easily and quickly be fixed or prevented. I have put together a post on my blog which outlines some basic best practices and troubleshooting of the vApp.
http://www.storagegumbo.com/2012/05/vc-ops-basic-vapp-troubleshooting.html
If I have to offer one single bit of advice it would be to make sure you update to the latest version because many bug fixes are included in 5.0.1 and 5.0.2 including some "self-healing" capability with broken vApps.
Visit my blog for vCloud Management tips and tricks - http://www.storagegumbo.com
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