The first thing that is needed for all the lines is a clear statement on their future.
Either they should close or there should be a 10+ year commitment to them.
Without that nobody will commit to using them for commuting purposes and nobody will want to invest in the lines because the money could well just be wasted.
What's needed then? Loads
Aside from safety, initial investment needs to focus on reducing operational costs. e.g. How much money can be saved by removing level crossings? Get them down and the case against closing diminishes.
Improved timetabling. Not really getting faster, but getting people to arrive at the time they want. Faster would also be better, but it's primarily an issue for two of the lines (Nenagh-Limerick and Wexford-Dublin).
A few specific to the Nenagh line.
There needs to be a bus service from Castleconnell to Limerick via UL that meets the morning arrival in Castleconnell and drops to the evening departure. It may take a couple of people off the train, but it makes commuting to UL on that line more viable.
Is there any practicality in tying up with a P&R solution on either the M7 or N24?
Limerick Council needs to start looking at where commercial investment is directed and seek to get central office buildings rather than suburban office parks. This isn't just to keep the trainline open either. It also benefits central retail businesses and a broader public transport strategy. Now that there is no longer a county council looking to cannibalise business, there may be some hope on this.