On my quest to find nice ways of commuting, I just explored this one from Kalkara to the University in Msida. It includes on the way a coffee at the Cafe Cordina in the morning, or in the evenings a glass of wine in the Baccara Gardens, overlooking the Grand Harbour from the Saluting Battery. This makes every commute a small adventure, and the journey goes as follows:

10 min or 40 min past the hour, leave Kalkara and walk through the Birgu Ditch which is the West part of the Fortifications of Birgu. Should the gate be locked in the early morning, follow the road (equal walking time, just less spectacular).
Full or half of the hour, take the ferry from the Cospicua Pier and cross the Grand Harbour to the Valletta Waterfront Pier (takes 15 minutes)
Cross Valletta by foot, 30 minutes are enough to include the above mentioned coffee on the way. You may take the lift up for EUR 1,50 (the way down is free).
15 min and 45 min past the hour, take the ferry to Sliema. You will land at "The Strand". Cross the road and you will see a bicycle renting station operated by Nextbike Malta. Download and install the application and register your account beforehand.
Cycle from the Sliema Nextbike Station about 5 minutes to the Station of the University Sports Complex. The bike rental under 30 minutes is free (as of December 2016). Lock and return your bike and cross the underpass up the hill and you are on the Campus of the University of Malta. A campus map can be downloaded here.

The commute takes you 85 minutes. You can easily turn around the schedule for the way back, by using the ferry schedule leavelets, which you may download here. Here you can also see the limits of the ferry schedule in the morning and at night. Not the shortest way, but a nice one.

After 15 minutes walk, exiting the Birgu Ditch

Less than 5 minutes more walk: The ferry between Cospicua (the Three Cities) and Valletta Waterfront leaves every full and half hour and takes 15 minutes to Valletta.

The way to work, passing more interesting vehicles than cars.

Nextbike station in Sliema, opposite the ferry pier.

The campus of The University of Malta on a winter day.