The big difference between v3 and v5 is ability to autoroute on the PC using v5. With v3 you do not need to use your PC's hard drive to store the maps. You build your map sets in Mapsource and insert the appropriate CD to transfer them to the GPS. I upgraded to v4.02 for the autorouting, and the maps were updated for a new road in my home town. So if you don't have many new roads around you and you don't need autorouting, plus you'd rather not fill up your hard drive with map regions in order to get the maps to your Legend...v3 would be a good choice.
Almost forgot...the Map Sets are larger in the v3. I think about 2 - 4 MB per set since they include a larger area. The v4.02 & I assume v5 have smaller map set sections under 1MB a piece. I had an 8MB expansion chip for my eMap and I think I could generally only get 2 map sets loaded to it before I filled up the memory.
Once you have Mapsource installed off any Mapsource CDs, updates to the Mapsource program are free from Garmin. The latest release of Mapsource is v5.4. Note that this does not update your maps, just the program that lets you see the maps on your PC and interfaces map, waypoint, route, & track data with your GPS.