With the introduction of Google Plus. Managing multiple gmail accounts has become a big pain in the ass. What I have done is consolidated all my email accounts into my main gmail account that I use for G+, analytics, etc. This process expects that you have one main gmail account such as "example@gmail.com" and one or more Google App accounts "henry@example.com". This solution may not work for you but it has helped me a lot.
The end result of this setup is that all your email goes to one inbox but it is clear by the use of labels where each email has been sent to and replies to such email will default to the address the email has been sent to. Also, you will be able to send email from any of your Google App accounts without leaving your main Gmail web client with the default of your choice. Yay!
This is broken into two steps. Incoming and Outgoing. Lets start with the Incoming mail...
Go to Settings > Forwarding and POP/IMAP in your Google App account and forward email to example@gmail.com. Have all your mail set to "mark as read" (you will have to go through a verification process with your example@gmail.com account).
Repeat this step for each of your Google Apps email accounts.
Go to Settings > Filters in your example.gmail.com account and create a filter for each account your are having forwarded. Have a unique label for each email account.
Repeat this step for each of your Google Apps email accounts using a different label for each account.
Go to Settings > Accounts and Import in your example.gmail.com account. Under the "Send mail as:" section click the "Send mail from another address" button.
Select "Send through sintaxi.com SMTP servers" and set the SMTP Server as smtp.gmail.com and Username as your Google Apps email address (henry@example.com). It will ask you for your Google Apps password for that email address.
In the same tab set When replying to a message: to "Reply to same address the message was sent to"
In the same tab set a default account you want email to be sent from (note - when you go to compose a new message you will have a dropdown giving you the choice of which email you want the message to be sent from).
