Just looking at some of the possibilities for improving tkl core on a per appliance basis. Some of the key changes would be in the file systems used for appliances. Its an area that doesn't get much attention but can greatly increase speed and/stability of an appliance. Think about XFS, ReiserFS/Reiser4, BTRFS as well as the usual EXT3/4.
Also another application which may help you would be SystemTap or LTTng . They are immature versions of DTrace but they will help in finding bottlenecks in your appliances and your customers deployments.
.....Also, I know this has been said quite a bit but.... Switching to 64bit does have advantages.... And to be honest even newer Atom processors are 64bit capable...
The appliance lineup could be changed a bit to make it a bit more SME/mini web startup friendly. (e.g. The inclusion of noSQL databases and web servers. CouchDB and NGNIX come to mind, along with Sinatra for Ruby on Rails). Many modern web apps don't need the power of a web server. Also many web dev's cant use SQL DBs or even need to use their full functions.
Anyway these are just my few cents; hope they're of some help
let me know what you think and i could help with a list of new apps (aimed at speed and flexibility) if you would like.