I don't know what your budget is, but the two "industry standards" are
Sage Timeslips and
Billquick. Both are feature rich - and expensive. At approximately $500 each they're usually too pricey for most small businesses and freelancers.
Links:
Timeslips:
http://www.timeslips.com/Billquick:
http://www.bqe.com/Default.asp---------------------------------
BillingTracker Pro ($89-single user) is a capable, simpler, and significantly less expensive all-in-one system.
Link:
http://www.billingtracker.com/---------------------------------
If you're really strapped for cash, you can combine a free invoicing system with a free time tracking application. This would involve a little extra work for you since the two systems wouldn't be integrated. You would first need to track your time, and then generate a report for creating your client invoice.
One excellent free time tracker is
HourGuard Free Timesheet Recorder 
Link:
http://www.nchsoftwa...timesheet/index.htmlThis could be coupled with a free accounting package like
MS Accounting Express or
GNUCash:
Microsoft Accounting Express http://office.micros.../FX101729681033.aspxGNUCashhttp://gnucash.org/-----------------------
I would suggest downloading trial copies of anything before you buy it.
I'd especially recommend you download Billquick's 30-day trial just to get an idea of what a heavy-duty pro time billing app is like. You could then use that experience to evaluate anything else you're looking at.
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I think Dormouse made a very astute observation earlier:
What I wouldn't use them for (again) is a situation where the business is essentially selling hours/minutes of time. Too complex, too unrelated to the main activity.
Whatever you decide to get, make an effort to keep it as simple as possible. Anything that distracts you from "taking care of business" just isn't worth it. Better to loose a few billable minutes than get bogged down for hours running an overly complex accounting package.
FWIW: I used a basic Excel spreadsheet to track my billable time and expenses for the first three years I was in business. And I did my billing with a $39 Invoice/Estimate package I picked up at Staples. And that simple combination worked out just fine until I needed to add employees.
