Yes, as ASW mentioned above, there are alot of angles to look at when valuing a business.
Gross Margin and Net Income are hot items (but definitely NOT the only items) to look at but like mentioned above, other things that the business has such as customer relationships, computer and software technology developed in house, etc. lead to goodwill.
The aging of the accounts receivable, amount of debt on the balance sheet as well as historical financial data help to determine a business value.
I was in public accounting for 10 years and am a senior manage of finance for a major logistics company where we have purchased 5 companies since 2002.
There are accounting firms such as E&Y who have specialized teams that perform business valuation services.