Quickbooks is based on having customers (for invoicing) and vendors. However as a web app/software/iphone dev company I can't manually enter in all the customers and we really don't have vendors.
Most of the expenses are reoccurring fixed costs (such as hosting, salaries, etc...) and I don't need to (usually) issue invoices...
I need to start keeping better records of expenses/income and am wondering if QuickBooks is the best solution? Or what other startups are using?
If your only customer is the Apple App Store, well, you have one customer. You certainly have vendors. Anything you buy for the business is bought from a vendor.
If you're paying salaries, you have to calculate payroll taxes (and then pay them). This is pretty complicated. Even the biggest companies outsource it to companies like ADP or PayChex, who don't do a very good job. Intuit's payroll service, built into QuickBooks, will do a great job of calculating payroll taxes, withholding them, filing them with the government, etc. Don't try to play that game where your employees are "1099 contractors." You WILL get audited for this (we did).
You can try to roll your own accounting software, if your time is worth $0.00001/hour, or you can just do what almost every other small business does... use QuickBooks, learn how to do basic bookkeeping, and hire an accountant to check in and make sure you're doing everything right. Tax evasion is a pretty stupid problem to have, especially if it's not intentional!