Marta,
We use a few software programs that integtrate well with each other and let our VA's track time by client and enter tasks.
Avalanche- Time Tracker tool. This widget is free and available through yahoo widgets. It connects with our Basecamp project management software which we keep all of our clients(projects) and the tasks.
Basecamp- online software through 37 signals. This software keeps all of our client projects and lets us collaborate with clients. They can assign tasks and upload files. It also keeps track of all of the time entered through the Avalanche widget. Your VA team can also enter time directly into Basecamp.
Freshbooks- I know this software has already been mentioned. It's a great invoicing tool and it will pull all of the time and notes from Basecamp into a detailed invoice for your clients. Credit card and Paypal can also be enabled so clients can pay their invoice online. The downside with Basecamp is that if you choose the detailed invoice with all time showing as a individual line item you will need to enter the rate for each line item.
Hope this helps.
Best regards,
Heather
Virtual Help Resources
www.virtualhelpresources.com