Things that can help you run the game more smoothly:
Ability to lookup rules quickly: An HTML version of the SRD is one possibility. That's a little hard to add info to. Programs like DM's Familiar (mine), DM Genine, and RPM do it as well. The ability to search this info (what are all the 3rd level wizard spells I have in the computer) and the ability to cross-reference are nice (example: DM's Familiar let's you enter spells to a creature. You can double-click the spell to pull it up for more info. The others probably do this as well.
The ability to import/export information from this is needed if you use rulebooks beyond the SRD.
Combat Management: Let the computer manage initiative and who's turn it is. Ideally it should also track durations of spells and such to tell you when it's done. If you'll let the computer roll dice for you, you're combats will go much faster. Doing a claw/claw/bite/tail slap/wing slap with one click of a button is a good thing.
Ideally, the combat manager should handle all the buffs & nerfs that are going on. Especiall in a high level campaign. DM's Familiar, DM Genie, RPM, etc. do these things. It makes the game run much faster.
Notes: Some way to organize your notes. Word can do it. Again though the search and cross-reference abilities are the time savers: Write an adventure, be able to drag & drop creatures to it, be able to drag & Drop from the adventure to the combat board, etc. DMF, DM Genie, RPM can do things like this.
Those are the things I find, in game, can really make things run smoother. All the programs have free demos. Take a look and see what you like.