As a startup freak myself, I am always looking for new ways to make the company better and communications between the teams easier. I like Slack as a communications tool as well as Asana. HipChat is pretty slick for instant messaging and integration with inbound customer service live chatting forums. As far as CRM I happen to like Close.io which offers calling directly from the CRM but also tracking of all emails in & out. Easy User Interface and they are slowly getting the tools needed to compete with the big boys.
Well, Excel is still the world's number one ERP, but putting that aside for now, I would think that the biggest issue entrepreneurs face is finding IT tools that are relevant to the size of their business. They need to set themselves up to handle growth when it inevitably occurs, but many of the systems they would ultimately end up with when they are mature, are far too cumbersome and full featured to support a startup.
Therefore, they end up with tools that are really most suitable for freelancers or independents, and can only take them part of the way. Additionally, they often have trouble finding operational systems that are integrated (accounting/project management/time tracking/production management/resource management etc.) so they end up defaulting back to spreadsheets and Google docs to try and piece together a view into their organisation.
As an early stage startup, I would be expecting to track cash flow on a micro timescale, production/project management and cycles, profitability and customer acquisition metrics as these are the areas where there will be (should be) the most variability and evolution IF the data is available and the company can easily see where a pivot may be required.
I have helped a number of small businesses in growth phase, and startups, piece together integrated operations foundations that cost very little and provide a working foundation that will get them to the point where they start to see enough volume in their business that necessitates a transition to more robust systems. I've also worked with more mature organisations to take them through a software selection process once they are ready to mature.
It's natural for a startup to progress and mature its systems, but the trick is to set them up from the beginning such that the DATA is easily accessible and transferrable once growth happens.
Happy to chat further - feel free to reach out directly.