You don't have to. If you do a Time Machine backup and restore from it, you should have no need to "choose" anything, or "restore" anything apart from Pro apps like Microsoft Office, Adobe pro apps, that sort of thing. If you do a bootable clone and restore from that, you won't even (most likely) have the issue with the pro apps.
For some reason, every last remaining Snow Leopard hold out has finally decided that now is the time to upgrade. While we say "welcome," we've seen a lot of similar questions about this here, so here is something I wrote for the benefit of another "jumper":
Be aware that making such a big jump (five major upgrades later ... you really should have updated before this) is going to break A LOT of your software. I don't say this to discourage you, I say it because its going to happen. Anything you're using that relies on PPC code is going to be irreparably broken, everything else is going to need updates (which should be mostly free). You'll know the ones that are PPC apps -- the upgrade will put them in a folder, and/or they will have a big NO sign across the icon. Those will need to be either upgraded or replaced.
Of course you should create a working clone backup of the system as it is now to an external drive, and I'd suggest using Carbon Copy Cloner (free 30-day trial, then you should buy it because it is fantastic).
1. Make a backup using
at least Time Machine, but a clone backup to an external using Carbon Copy Cloner or something like it would be even better or also a good idea
in addition to the Time Machine backup.
2. *PERSONALLY* check (don't go by web reports) that your key software that you must have is as up-to-date as possible, and if you're not 100 percent certain contact the developer for compatibility assurances -- you are skipping five major upgrades! In particular, if you're heavily reliant on iPhoto you MUST be bang-up-to-date with version 9.6.1, and if you're heavily reliant on Outlook or MS Office generally you'd be best advised to wait a bit (this seems to have since been sorted out mostly, but not fully). Also double-check about audio plug-ins you might be using with music-making programs like Pro Tools, and check on any Firewire audio devices that require drivers -- a lot of that stuff broke because of well-publicized changes Apple has made to the kernel and FW and AUs and such.
3. As is always a good idea, run
OnyX for your current version of OS X to optimize the maintenance before upgrading, and remember to toss that version and get the new El Capitan version before trying to run it once you've upgraded.
4. Once El Capitan has installed, run the Mac App Store and install any suggested updates.
If you want to keep that old machine going a while longer, I'd suggest considering the possibility of replacing the boot drive with an SSD down the road. That will keep it nice and snappy, and increase the resale value towards your next machine, which you will probably want/need in a another year or two.