Air Portugal - Tap operate regular flights from Malaga to Lisbon but the one way ticket price is ridiculous - in the order of € 364 per person at the end of June 2008. You may get something cheaper by buying returns.
A combination of low-cost flights involving airlines such as Spanair/ Clickair/Easyjet/Vueling on the route from Malaga to Lisbon via Barcelona or Madrid may be your best bet by air.
By long distance coach, www.alsa.es operate an overnight daily bus service as follows: