Need practical advice on test automation

There is a system:

• A wide variety of applications on the server (planned continuous replenishment)
• The client (two versions — java and web/flash) through which a user runs applications and manages

Task:

To find the best (fast and reliable) way to automate the testing process.
Tested each application (roughly speaking, runs through both versions of the client and is checked).
When you add a new application (or a dozen) you need to quickly and efficiently test their behavior when using both clients. The goal is the behavior of the application when run through the client should be identical (if possible) to his behaviour in normal startup.

Ask for advice based on experience — what tools are most practical and effective for this problem?
How best to organize the work?

Update: the Question concerns how specific tools used, and experience of organising such things.
If someone like that did, write 2-3 words, how to organize this. Thanks in advance!