1. Setting a deadline for task and being alerted – can be done with standard setup.

2. Showing dependencies – here, I'm not sure here and I can no longer check. There were interlinks between tasks but it wasn't anything close to MSP-like dependencies of all sorts, so I can't deifnitely say yes or no here.

Anyway I can say I worked with Jira as a PM tool by myself and it was sufficient for our needs. Of course we weren't doing rocket science but to organize few dozen of people working on several projects Jira was enough in terms of functionality (given that we got source code, we could have added anything if we needed too). And in terms of easiness of use, well, it isn't so hard to beat MS Project especially when it comes to collaboration.

It all depends on size on complexity of projects you're working on. As you've said – you're in top 10% MSP users in terms of functionality you need from the tool. I wasn't anywhere close.

Do these much less tools provide for a network of activities? How about setting deadlines and be informed that you've messed it? How about showing external dependencies for "parts" arriving from someone else.

What's look like a project management tool – Jira – is labeled bug tracking. If you're using that definition, then absolutely MSP is over kill.

But not sure bug tracking is the same as PM. Bug Tracking and fixing sounds a lot like "level of effort" to me. No fixed budget delivery time, resource level etc.

This is an example (a friendly one) of overloaded the work "project management" and "project management tools."

We were just sending out mpp files through email since basically the main goal was to agree project plan with customers. Lack of MS Project installed wasn't an issue in our case because we worked for big telecommunication companies so everyone who would use mpp file had MS Project installed on their machine.

By the way: I must admit amiproject looks very nice. I'm not sure however how often lack of MS Project installed is an issue among stakeholders. My guess is they usually have it already installed. On the other hand you should take a look on a rather typical situation when PM prepares schedule/project plan in MS Project and send it out to developers who don't have the tool (why should they anyway?) Of course tasks would be imported to some kind of tool which supports task management but it's usually helpful to visualize the whole project on Gantt chart.

In my previous company we covered internal project management-related processes with Jira and it worked really fine. We didn't rule out MS Project completely but we used it mostly in communication with our customers. Within the team there was no need to use it.

I'm sure neither Jira nor other web-based tools I've used so far wouldn't be suitable in your case, but there are all sorts of environments with different requirements when it comes to PM tool. By the way, at the moment my most valuable tools are whiteboard, set of markers and bunch of sticky notes. I don't need much more to manage a project in a way I believe is credible.

Anyway, for complex environments MS Project even at full price isn't expensive. For small ones there are programs like MAPS or BizSpark which give you tons of Microsoft licences, including Project, basically for free. Like one of my business partners used to say: if there's will there's a way.

There are those claiming replacement fro MSP at a lower price, but none actually provide features needed for managing projects in any credible manner.

Project Server provides collaboration through PWS and other sharepoint services. As well there are EPM add ons for Project Server and Share Point that provide most of what is needed for virtual teams.