Certainly. I use Morning Flight gold edition . It is PC desktop only. No Mac version. No web version. Very affordable. But if you need multi-person access, it may not be a good solution. As for job tracking, you can mark a job Design, Awaiting OK, Prepress, Press, Post Press, and Delivered. You can also print out an Open Jobs list which is nice. One problem though, if you invoice the job it's locked so you can't change the status in the job tracker. Not a problem for most customers that pay upon receipt or Net 30 but those that want an invoice up front... Other shops that use Morning Flight also use Trello for tracking jobs. I used Trello for awhile but gave up after a few years. I'm just not that big of a shop to warrant the time spent creating a "card" and moving it around the digital board. But it was awesome, none-the-less.
I use Business Importer to get the invoices into Quickbooks Online which costs about $120 for the year. Morning Flight can export a CSV file and the Business Importer brings it into QB. A lot of clicking but it beats typing especially when you have a dozen invoices to import. Morning Flight is a great price calculator and keeping track of job details for repeat orders. It's super easy to recall a job, change any specs, etc. A lot of my customers rely on me to remember job details. I've been using it since beta testing it in 2008 so I'd be happy to talk over the phone about it and answer any questions.
Last year, I did attempt to try a web based MIS system. After years of research, I decided on PrintLogic, based in Ireland. Super affordable and had awesome features. What I didn't like was how it calculated prices and didn't seem to be very good at repeat jobs (if any of the specs changed, you had to start over with a new quote). Gave up on it after five months. A couple really cool features was it's ability to mass email any of your customers directly from within the software. You could also create custom price lists for specific customers.