If for some reason you don't want all your desktop bookmarks to sync to your phone (too many bookmarks, privacy issues, bookmarks that won't work on the phone anyhow, etc.), here's a fairly easy way (once you get the hang of it) to create a separate bookmarks "profile" for the iPhone.
Note: This is for Mac users. It probably works fine on a PC, I just don't know the method. Warning...this will replace all the bookmarks currently on your iPhone, with a tidier set of iPhone-only bookmarks. If this sounds too scary to you, don't do it. It would be best to sync your phone, including bookmarks, before you begin this process. Once you sync, turn off auto sync temporarily.
1. In Safari on your Mac, make a new bookmark folder, call it iPhone, or whatever you like. Drag all the bookmarks you want on the phone into the folder. CMD+drag to copy them (recommended) instead of moving them.
2. Once you have all the bookmarks you want in the iPhone folder, drag the folder to the desktop. This copies all the iPhone bookmarks there for safe keeping (and re-importing later).
3. Quit Safari. In the finder, go to Your Home Folder/Library/Safari. Drag "bookmarks.plist" to the desktop, or anywhere outside of the Library/Safari folder. Just remember where you put it. And DON'T put it inside the iPhone folder on your desktop.
4. Start Safari again. You'll notice you have no bookmarks at all. Fear not. Open the bookmarks view. From your desktop, drag the iPhone bookmarks folder you made onto the RIGHT side of the bookmarks pane. Now you have Safari loaded with only your iPhone bookmarks. Quit Safari.
5. Fire up iTunes. Don't sync just yet. In the "Info" tab, scroll to the bottom of the screen and check the box to replace the iPhone's bookmarks for this sync. Now you can sync. Verify that the iPhone received your nice tidy folder of bookmarks.
6. In the finder, go back to Your Home Folder/Library/Safari. Drag "bookmarks.plist" INTO the iPhone folder you made on the desktop...this is where you will keep your iPhone bookmarks.plist from now on. On your desktop, or wherever you dragged it initially, find the ORIGINAL bookmarks.plist and drag it back into Your Home Folder/Library/Safari. Fire up Safari and all your regular bookmarks are back in place.
You're done. The only catch is, if you want to sync your new tidied up iPhone bookmarks every time you sync, you'll have to do the .plist swap first. Just make absolutely sure you drag the bookmarks.plist from the Library/Safari to a safe place before you drag your iPhone version in, otherwise you could lose all your bookmarks. If you're nervous about it, create an archive of the .plist and email it to yourself, or put it on a thumbdrive.
Swapping plists only takes a few seconds, but I find it saves a lot of bookmark navigation time on the phone if you have tons of bookmarks on your Mac.
Note: This is for Mac users. It probably works fine on a PC, I just don't know the method. Warning...this will replace all the bookmarks currently on your iPhone, with a tidier set of iPhone-only bookmarks. If this sounds too scary to you, don't do it. It would be best to sync your phone, including bookmarks, before you begin this process. Once you sync, turn off auto sync temporarily.
1. In Safari on your Mac, make a new bookmark folder, call it iPhone, or whatever you like. Drag all the bookmarks you want on the phone into the folder. CMD+drag to copy them (recommended) instead of moving them.
2. Once you have all the bookmarks you want in the iPhone folder, drag the folder to the desktop. This copies all the iPhone bookmarks there for safe keeping (and re-importing later).
3. Quit Safari. In the finder, go to Your Home Folder/Library/Safari. Drag "bookmarks.plist" to the desktop, or anywhere outside of the Library/Safari folder. Just remember where you put it. And DON'T put it inside the iPhone folder on your desktop.
4. Start Safari again. You'll notice you have no bookmarks at all. Fear not. Open the bookmarks view. From your desktop, drag the iPhone bookmarks folder you made onto the RIGHT side of the bookmarks pane. Now you have Safari loaded with only your iPhone bookmarks. Quit Safari.
5. Fire up iTunes. Don't sync just yet. In the "Info" tab, scroll to the bottom of the screen and check the box to replace the iPhone's bookmarks for this sync. Now you can sync. Verify that the iPhone received your nice tidy folder of bookmarks.
6. In the finder, go back to Your Home Folder/Library/Safari. Drag "bookmarks.plist" INTO the iPhone folder you made on the desktop...this is where you will keep your iPhone bookmarks.plist from now on. On your desktop, or wherever you dragged it initially, find the ORIGINAL bookmarks.plist and drag it back into Your Home Folder/Library/Safari. Fire up Safari and all your regular bookmarks are back in place.
You're done. The only catch is, if you want to sync your new tidied up iPhone bookmarks every time you sync, you'll have to do the .plist swap first. Just make absolutely sure you drag the bookmarks.plist from the Library/Safari to a safe place before you drag your iPhone version in, otherwise you could lose all your bookmarks. If you're nervous about it, create an archive of the .plist and email it to yourself, or put it on a thumbdrive.
Swapping plists only takes a few seconds, but I find it saves a lot of bookmark navigation time on the phone if you have tons of bookmarks on your Mac.