Can we use other companies' logos in our software?

To add to what Mr. Weinreib correctly highlights, you want to avoid creating a likelihood of confusion as to the source or sponsorship between your use of those logos / trademarks and that of the logos / trademarks' owners. Using another’s mark in a comparative or nominative fashion (e.g., de minimis or "nominative fair use") will generally not be considered actionable infringement, though to be such “fair” use will generally require that the cited product/service cannot be otherwise identified without the mark, you only use a minimum portion of the mark (i.e., no logos, probably), and you go out of your way to disclaim any association between you and the marks’ owners (e.g., use ®, “__ and __ are registered trademarks of XYZ Inc.,” etc.). You may be able to accomplish this without trying to negotiate a license, but that will depend on very fact-specific information best suited for a conversation with IP counsel in private.