There was a change several months back to allow saving path explorer data to avoid having to recompute it upon every load or server join. The data usage in an uncompressed save file would be approximately 6 bytes per ordered pair of halts, for each category/class, plus a bit extra for work-in-progress. For example, if you have 5 passenger classes, 2 mail classes, 5000 halts with passenger service and 4000 with mail service, then that would give a total contribution to the save file size of 5*5000*5000*6+2*4000*4000*6 bytes, i.e about 942MB. However, save files are usually compressed, which reduces this size somewhat.
I think you should be able to switch off saving path explorer data by setting save_path_explorer_data = 0 in simuconf.tab, although I'm not sure whether this applies to existing games - you may need to edit the setting ingame to do that (I'm can't remember right what key you need to reach that settings menu).
