Having been asked about this more than once recently, by companies who don't yet have any users or customers :

Early stage patent applications
If you are contemplating applying for a patent for the first time for your startup company, there are several considerations.

• Getting a patent awarded typically takes several years of elapsed time.
• The obvious costs are the fees to be paid to the patent office, and the fees for a patent attorney to help with preparation.
  Search for 'cost of applying for US patent' to get approximate numbers and guidelines.
• Don't ignore the cost of your time; explaining engineering ideas to attorneys is not easy. Seriously consider whether you'd be adding more value by explaining your ideas to potential customers instead.

Brad Burnam, from Union Square Ventures, has a useful essay; in the comments, he says "In the world of web services, where we invest, you will have succeeded or failed long before a patent is approved, so it often does not make sense to invest in the process."

In addition, the question to ask is not so much what the upfront costs are, but if you could actually afford to defend a patent if you had one. Can you grow the company enough to afford settle a patent suit ?

Cisco Systems had only one patent for several years after the IPO
Cisco's approach to patents was not to spend any time or money with patent lawyers until they were about to do the IPO (in 1990). As part of that process they patented the IGRP routing protocol - and there were no more patent applications for several years, until they got to the point where they needed patents as a currency to exchange with competitors in cross-license agreements. Sequoia Capital did not require them to have applied for a patent as a pre condition of their funding. The thinking was that by the time a competitor had read the patent application and or reverse engineered the hardware, that Cisco would have developed something new and the patented product would have been superseded. Although Cisco is nominally a hardware company, in fact the hardware was perceived internally as a method for packaging software - that was the real added value.

Recently, there's been an upswing in informed opposition to software patents. Brad Feld, at Foundry, is keenly interested in the problems with the patent system and has a series of detailed posts covering the issues.

References
Brad Burnam, USV on software patents
Brad Feld, Foundry Group - series of patent posts
US patent office process chart